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Giselle Moreira M, Guimarães Oliveira AG, Ul Haq I, Pinheiro de Oliveira TF, Alonazi WB, Fonseca Júnior AA, Nobre Junior VA, dos Santos SG. Droplet Digital PCR for Acinetobacter baumannii Diagnosis in Bronchoalveolar Lavage Samples from Patients with Ventilator-Associated Pneumonia. Antibiotics (Basel) 2024; 13:878. [PMID: 39335051 PMCID: PMC11429060 DOI: 10.3390/antibiotics13090878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 09/02/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
Advanced diagnostic technologies have made accurate and precise diagnosis of pathogens easy. Herein, we present a new diagnostic method, droplet digital PCR (ddPCR), to detect and quantify Acinetobacter baumannii in mini bronchoalveolar lavage (mini-BAL) samples. A. baumannii causes ventilator-associated pneumonia (VAP), a severe healthcare infection affecting patients' lungs. VAP carries a high risk of morbidity and mortality, making its timely diagnosis crucial for prompt and effective management. Methodology. The assay performance was evaluated by comparing colonization data, quantitative culture results, and different generations of PCR (traditional PCR and Real-Time PCR-qPCR Taqman® and SYBR® Green). The ddPCR and qPCR Taqman® prove to be more sensitive than other molecular techniques. Reasonable analytical specificity was obtained with ddPCR, qPCR TaqMan®, and conventional PCR. However, qPCR SYBR® Green technology presented a low specificity, making the results questionable in clinical samples. DdPCR detected/quantified A. baumanni in more clinical samples than other methods (38.64% of the total samples). This emerging ddPCR technology offers promising advantages such as detection by more patients and direct quantification of pathogens without calibration curves.
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Affiliation(s)
- Mirna Giselle Moreira
- Departament of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Pampulha, Belo Horizonte 31270-901, Minas Gerais, Brazil; (M.G.M.); (A.G.G.O.)
| | - Anna Gabriella Guimarães Oliveira
- Departament of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Pampulha, Belo Horizonte 31270-901, Minas Gerais, Brazil; (M.G.M.); (A.G.G.O.)
| | - Ihtisham Ul Haq
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland;
- Joint Doctoral School, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
- Postgraduate Program in Technological Innovation, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Tatiana Flávia Pinheiro de Oliveira
- Federal Agricultural Defense Laboratory of Minas Gerais, Av. Rômulo Joviano s/n, Centro, Pedro Leopoldo 33600-000, Minas Gerais, Brazil; (T.F.P.d.O.); (A.A.F.J.)
| | - Wadi B. Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Antônio Augusto Fonseca Júnior
- Federal Agricultural Defense Laboratory of Minas Gerais, Av. Rômulo Joviano s/n, Centro, Pedro Leopoldo 33600-000, Minas Gerais, Brazil; (T.F.P.d.O.); (A.A.F.J.)
| | - Vandack Alencar Nobre Junior
- Interdisciplinary Center for Research in Intensive Care Medicine (NIIMI), Faculty of Medicine, Federal University of Minas Gerais, Av. Prof. Alfredo Balena 110, Santa Efigênia, Belo Horizonte 30130-100, Minas Gerais, Brazil;
| | - Simone Gonçalves dos Santos
- Departament of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Pres. Antônio Carlos 6627, Pampulha, Belo Horizonte 31270-901, Minas Gerais, Brazil; (M.G.M.); (A.G.G.O.)
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Petraitis V, Petraitiene R, Kavaliauskas P, Naing E, Garcia A, Zigmantaite V, Grigaleviciute R, Kucinskas A, Pockevicius A, Stakauskas R, Walsh TJ. Development of rabbit models of ventilator-associated bacterial pneumonia produced by carbapenem-resistant Pseudomonas aeruginosa. Antimicrob Agents Chemother 2024:e0020524. [PMID: 38687014 DOI: 10.1128/aac.00205-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Ventilator-associated bacterial pneumonia (VABP) is among the most intractable of carbapenem-resistant Gram-negative bacterial infections. New antimicrobial agents are critically needed for the treatment of VABP. However, current conventionally used animal model systems are inadequate to meet this challenge. We, therefore, developed rabbit models of VABP caused by carbapenem-resistant Pseudomonas aeruginosa. Persistently neutropenic New Zealand White rabbits were used throughout the study. The early-phase intubated model (0-24 h) received mechanical ventilation, while the late-phase intubated model (72-96 h) was ambulatory. The following outcome parameters were studied: survival, residual tissue bacterial burden (CFU/g), residual BAL bacterial burden (CFU/mL), lung weights, pulmonary lesion score, histology, O2 saturation, radiographic imaging, and histology. Each anesthetized rabbit received a predetermined endotracheal bacterial inoculum, and ventilators were set to FiO2 = 40% and PEEP = 8 mmHg. Within the first 12 h post-inoculation, mean bacterial burdens in lung tissue and BAL fluid, respectively, were established at approximately 107 CFU/g and 106 CFU/mL, persisted through 24 h in the early-phase model and increased in the late-phase model to approximately 108 CFU/g and 107 CFU/mL. Mean max SpO2 was ≥98 mmHg, and mean nadir SpO2 was ≥68 mmHg. Serial thoracic radiographs demonstrated progressive multilobar pneumonic infiltrates. Lung histology revealed progressive focal bronchopneumonia, coagulative necrosis, intra-alveolar hemorrhage, alveolar epithelial cell necrosis, and bacterial microcolonies. The new rabbit model of VABP produced by carbapenem-resistant Pseudomonas aeruginosa recapitulates the pathophysiological, microbiological, diagnostic imaging, and histological patterns of human disease by which to assess critically needed new antimicrobial agents against this lethal infection.
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Affiliation(s)
- Vidmantas Petraitis
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine of Cornell University, New York, New York, USA
- The Biological Research Center, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ruta Petraitiene
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine of Cornell University, New York, New York, USA
| | - Povilas Kavaliauskas
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine of Cornell University, New York, New York, USA
- The Biological Research Center, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ethan Naing
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine of Cornell University, New York, New York, USA
| | - Andrew Garcia
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine of Cornell University, New York, New York, USA
| | - Vilma Zigmantaite
- The Biological Research Center, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ramune Grigaleviciute
- The Biological Research Center, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Audrius Kucinskas
- The Biological Research Center, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alius Pockevicius
- Department of Veterinary Pathobiology, Veterinary Academy, Pathology Center, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rimantas Stakauskas
- The Biological Research Center, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Thomas J Walsh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine of Cornell University, New York, New York, USA
- Center for Innovative Therapeutics and Diagnostics, Richmond, Virginia, USA
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Du C, Liao Y, Ding C, Huang J, Zhou S, Xu Y, Yang Z, Shi X, Li Y, Jiang M, Zuo L, Li M, Bian S, Xiao N, Li L, Xu Y, Hu Q, Li Q. Molecular serotyping of diarrheagenic Escherichia coli with a MeltArray assay reveals distinct correlation between serotype and pathotype. Gut Microbes 2024; 16:2401944. [PMID: 39292565 DOI: 10.1080/19490976.2024.2401944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/13/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024] Open
Abstract
Diarrheagenic Escherichia coli serotypes are associated with various clinical syndromes, yet the precise correlation between serotype and pathotype remains unclear. A major barrier to such studies is the reliance on antisera-based serotyping, which is culture-dependent, low-throughput, and cost-ineffective. We have established a highly multiplex PCR-based serotyping assay, termed the MeltArray E. coli serotyping (EST) assay, capable of identifying 163 O-antigen-encoding genes and 53 H-antigen-encoding genes of E. coli. The assay successfully identified serotypes directly from both simulated and real fecal samples, as demonstrated through spike-in validation experiments and a retrospective study. In a multi-province study involving 637 E. coli strains, it revealed that the five major diarrheagenic pathotypes have distinct serotype compositions. Notably, it differentiated 257 Shigella isolates into four major Shigella species, distinguishing them from enteroinvasive E. coli based on their distinct serotype profiles. The assay's universality was further corroborated by in silico analysis of whole-genome sequences from the EnteroBase. We conclude that the MeltArray EST assay represents a paradigm-shifting tool for molecular serotyping of E. coli, with potential routine applications for comprehensive serotype analysis, disease diagnosis, and outbreak detection.
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Affiliation(s)
- Chen Du
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Congcong Ding
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Jiayu Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Shujuan Zhou
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Yiyan Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Zhaohui Yang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Xiaolu Shi
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Le Zuo
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Minxu Li
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | | | - Na Xiao
- Laboratory Department, Yantian District Center for Disease Control and Prevention, Shenzhen, China
| | - Liqiang Li
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
| | - Qinghua Hu
- Microbiology Lab Office, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences and School of Public Health, Xiamen University, Xiamen, China
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Hauser S, Lazarevic V, Tournoud M, Ruppé E, Santiago Allexant E, Guigon G, Schicklin S, Lanet V, Girard M, Mirande C, Gervasi G, Schrenzel J. A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia. Microbiol Spectr 2023; 11:e0129423. [PMID: 37889000 PMCID: PMC10715005 DOI: 10.1128/spectrum.01294-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.
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Affiliation(s)
| | - V. Lazarevic
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | - E. Ruppé
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | | | | | - V. Lanet
- bioMérieux, Marcy-l'Étoile, France
| | - M. Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - C. Mirande
- bioMérieux, La Balme-les-Grottes, France
| | | | - J. Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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Van Goethem S, Van Lint P, Willems P, Van Herendael B, Hoet K. Value of pneumococcal PCR in respiratory samples for exclusion of pneumococcal pneumonia. JAC Antimicrob Resist 2023; 5:dlad115. [PMID: 37941720 PMCID: PMC10629468 DOI: 10.1093/jacamr/dlad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
Background Streptococcus pneumoniae is the main aetiological agent in bacterial pneumonia. Therefore pneumococcal PCR is often included in respiratory multiplex PCR panels, both commercial and in-house. But respiratory PCR results for S. pneumoniae are difficult to interpret due to frequent non-pathogenic colonization on the mucosal surface of the upper airways with pneumococci or to cross-reaction of the PCR target in non-pneumococcal streptococci. In this study we investigated the value of lytA gene pneumococcal PCR in patients presenting with pneumonia. Objectives To assess the utility of lytA gene detection for S. pneumoniae in a respiratory multiplex quantitative PCR (qPCR) panel for patients presenting with pneumonia. Methods A retrospective study was conducted for lytA gene results as target for S. pneumoniae in hospitalized patients who were diagnosed with pneumonia and for which a respiratory multiplex PCR panel was performed. Patients were classified as 'probable', 'possible' or 'unlikely' of having a pneumococcal pneumonia. Results A sensitivity of 71.4% and specificity of 89.6% were found, corresponding to a negative predictive value and positive predictive value of 97.6% and 34.2%, respectively, when considering 'probable' versus 'possible/unlikely'. In the PCR-positive cases we found a statistically significant difference in semi-quantitative Ct values between the 'probable' and the 'possible/unlikely' groups. Conclusions We conclude that a negative qPCR for the lytA gene in a respiratory sample is highly predictive of a negative S. pneumoniae culture and is possibly sufficient to exclude S. pneumoniae as a causative agent. Respiratory pneumococcal PCR has a high negative predictive value for pneumococcal disease but the positive predictive value is low.
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Affiliation(s)
- Sam Van Goethem
- Laboratory of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
- Hospital Outbreak Support Team, ZAS Hospital Network, Antwerp, Belgium
| | - Philippe Van Lint
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
| | - Philippe Willems
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
| | | | - Katrien Hoet
- Medical Microbiology Laboratory, GZA Hospitals Antwerp, Antwerp, Belgium
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Lalbiaktluangi C, Yadav MK, Singh PK, Singh A, Iyer M, Vellingiri B, Zomuansangi R, Zothanpuia, Ram H. A cooperativity between virus and bacteria during respiratory infections. Front Microbiol 2023; 14:1279159. [PMID: 38098657 PMCID: PMC10720647 DOI: 10.3389/fmicb.2023.1279159] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023] Open
Abstract
Respiratory tract infections remain the leading cause of morbidity and mortality worldwide. The burden is further increased by polymicrobial infection or viral and bacterial co-infection, often exacerbating the existing condition. Way back in 1918, high morbidity due to secondary pneumonia caused by bacterial infection was known, and a similar phenomenon was observed during the recent COVID-19 pandemic in which secondary bacterial infection worsens the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) condition. It has been observed that viruses paved the way for subsequent bacterial infection; similarly, bacteria have also been found to aid in viral infection. Viruses elevate bacterial infection by impairing the host's immune response, disrupting epithelial barrier integrity, expression of surface receptors and adhesion proteins, direct binding of virus to bacteria, altering nutritional immunity, and effecting the bacterial biofilm. Similarly, the bacteria enhance viral infection by altering the host's immune response, up-regulation of adhesion proteins, and activation of viral proteins. During co-infection, respiratory bacterial and viral pathogens were found to adapt and co-exist in the airways of their survival and to benefit from each other, i.e., there is a cooperative existence between the two. This review comprehensively reviews the mechanisms involved in the synergistic/cooperativity relationship between viruses and bacteria and their interaction in clinically relevant respiratory infections.
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Affiliation(s)
- C. Lalbiaktluangi
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
| | - Mukesh Kumar Yadav
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College, Aizawl, Mizoram, India
| | - Amit Singh
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
| | - Mahalaxmi Iyer
- Department of Zoology, Central University of Punjab, Bathinda, Punjab, India
| | | | - Ruth Zomuansangi
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
| | - Zothanpuia
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College, Aizawl, Mizoram, India
| | - Heera Ram
- Department of Zoology, Jai Narain Vyas University, Jodhpur, India
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Li J, Shang MY, Deng SL, Li M, Su N, Ren XD, Sun XG, Li WM, Li YW, Li RX, Huang Q, Lu WP. Development of a novel integrated isothermal amplification system for detection of bacteria-spiked blood samples. AMB Express 2023; 13:135. [PMID: 38019349 PMCID: PMC10686969 DOI: 10.1186/s13568-023-01643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/19/2023] [Indexed: 11/30/2023] Open
Abstract
Bloodstream infection (BSI) caused by bacteria is highly pathogenic and lethal, and easily develops whole-body inflammatory state. Immediate identification of disease-causing bacteria can improve patient prognosis. Traditional testing methods are not only time-consuming, but such tests are limited to laboratories. Recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) holds great promise for rapid nucleic acid detection, but the uncapping operation after amplification easily contaminates laboratories. Therefore, the establishment of a more effective integrated isothermal amplification system has become an urgent problem to be solved. In this study, we designed and fabricated a hermetically sealed integrated isothermal amplification system. Combining with this system, a set of RPA-LFD assays for detecting S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI were established and evaluated. The whole process could be completed in less than 15 min and the results can be visualized by the naked eye. The developed RPA-LFD assays displayed a good sensitivity, and no cross-reactivity was observed in seven similar bacterial genera. The results obtained with 60 clinical samples indicated that the developed RPA-LFD assays had high specifcity and sensitivity for identifying S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI. In conclusion, our results showed that the developed RPA-LFD assay is an alternative to existing PCR-based methods for detection of S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI in primary hospitals.
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Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Shao-Li Deng
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Min Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Xian-Ge Sun
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Wen-Man Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Yu-Wei Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Ruo-Xu Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China.
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China.
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Wang Q, Zheng S, Liu Y, Wang C, Gu B, Zhang L, Wang S. Isothermal Amplification and Hypersensitive Fluorescence Dual-Enhancement Nucleic Acid Lateral Flow Assay for Rapid Detection of Acinetobacter baumannii and Its Drug Resistance. BIOSENSORS 2023; 13:945. [PMID: 37887138 PMCID: PMC10605404 DOI: 10.3390/bios13100945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023]
Abstract
Acinetobacter baumannii (A. baumannii) is among the main pathogens that cause nosocomial infections. The ability to rapidly and accurately detect A. baumannii and its drug resistance is essential for blocking secondary infections and guiding treatments. In this study, we reported a nucleic acid fluorescent lateral flow assay (NFLFA) to identify A. baumannii and carbapenem-resistant A. baumannii (CRAB) in a rapid and quantitative manner by integrating loop-mediated isothermal amplification (LAMP) and silica-based multilayered quantum dot nanobead tag (Si@MQB). First, a rapid LAMP system was established and optimised to support the effective amplification of two bacterial genes in 35 min. Then, the antibody-modified Si@MQB was introduced to capture the two kinds of amplified DNA sequences and simultaneously detect them on two test lines of a LFA strip, which greatly improved the detection sensitivity and stability of the commonly used AuNP-based nucleic acid LFA. With these strategies, the established LAMP-NFLFA achieved detection limits of 199 CFU/mL and 287 CFU/mL for the RecA (house-keeping gene) and blaOXA-23 (drug resistance gene) genes, respectively, within 43 min. Furthermore, the assay exhibited good repeatability and specificity for detecting target pathogens in real complex specimens and environments; thus, the proposed assay undoubtedly provides a promising and low-cost tool for the on-site monitoring of nosocomial infections.
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Affiliation(s)
- Qian Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China;
- Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei 230036, China; (S.Z.); (Y.L.); (C.W.)
- Department of Clinical Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Shuai Zheng
- Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei 230036, China; (S.Z.); (Y.L.); (C.W.)
- Department of Clinical Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Yong Liu
- Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei 230036, China; (S.Z.); (Y.L.); (C.W.)
- Wan Jiang New Industry Technology Development Center, Tongling 244000, China
| | - Chongwen Wang
- Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei 230036, China; (S.Z.); (Y.L.); (C.W.)
- Department of Clinical Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Bing Gu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510000, China
| | - Long Zhang
- Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei 230036, China; (S.Z.); (Y.L.); (C.W.)
| | - Shu Wang
- Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei 230036, China; (S.Z.); (Y.L.); (C.W.)
- Wan Jiang New Industry Technology Development Center, Tongling 244000, China
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Ladas P, Porfyridis I, Tryfonos C, Ioannou A, Adamide T, Christodoulou C, Richter J. Aetiology of Community-Acquired Pneumonia and the Role of Genetic Host Factors in Hospitalized Patients in Cyprus. Microorganisms 2023; 11:2051. [PMID: 37630611 PMCID: PMC10458012 DOI: 10.3390/microorganisms11082051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/25/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Community-acquired pneumonia (CAP) remains the leading cause of hospitalization among infectious disease in Europe, and a major cause of morbidity and mortality. In order to determine and characterize the aetiology of CAP in hospitalized adults in Cyprus, respiratory and blood samples were obtained from hospitalized patients with CAP, and analyzed using Multiplex Real-Time PCR/RT-PCR, and ID/AMR enrichment panel (RPIP) analysis. Probe-based allelic discrimination was used to investigate genetic host factors in patients. The aetiology could be established in 87% of patients. The most prevalent viral pathogens detected were influenza A, SARS-CoV-2, and human rhinovirus. The most common bacterial pathogens detected were Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae. Antimicrobial resistance genes were identified in 23 patients. S. aureus was the most common AMR correlated strain in our study. A positive correlation was detected between bacterial infections and the NOS3 rs1799983 G allele and the FCGR2A rs1801274 G allele. A positive correlation was also detected between the TNF-α rs1800629 A allele and sepsis, while a negative correlation was detected with the ACE rs1799752 insertion genotype and the severity of pneumonia. In conclusion, the targeted NGS panel approach applied provides highly sensitive, comprehensive pathogen detection, in combination with antimicrobial resistance AMR insights that can guide treatment choices. In addition, several host factors have been identified that impact the disease progression and outcome.
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Affiliation(s)
- Petros Ladas
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
| | - Ilias Porfyridis
- Pulmonary Department, Nicosia General Hospital, Lemesou 215, 2029 Strovolos, Nicosia, Cyprus; (I.P.); (A.I.); (T.A.)
| | - Christina Tryfonos
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
| | - Anna Ioannou
- Pulmonary Department, Nicosia General Hospital, Lemesou 215, 2029 Strovolos, Nicosia, Cyprus; (I.P.); (A.I.); (T.A.)
| | - Tonia Adamide
- Pulmonary Department, Nicosia General Hospital, Lemesou 215, 2029 Strovolos, Nicosia, Cyprus; (I.P.); (A.I.); (T.A.)
| | - Christina Christodoulou
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
| | - Jan Richter
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, 2371 Egkomi, Nicosia, Cyprus; (P.L.); (C.T.); (C.C.)
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Cojuc-Konigsberg G, Moscona-Nissan A, Guijosa A, Mireles Dávalos CD, Martínez MEJ, Mújica Sánchez MA, Hernández Huizar VF, Durán Barrón MA, Gómez KV, Andrade-Galindo R, Ordóñez-Oviedo M, Brito GD, Vargas EB. Diagnostic accuracy of the BioFire® FilmArray® pneumonia panel in COVID-19 patients with ventilator-associated pneumonia. BMC Infect Dis 2023; 23:524. [PMID: 37559032 PMCID: PMC10413519 DOI: 10.1186/s12879-023-08486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Ventilator-Associated pneumonia (VAP) is one of the leading causes of morbidity and mortality in critically ill COVID-19 patients in lower-and-middle-income settings, where timely access to emergency care and accurate diagnostic testing is not widely available. Therefore, rapid microbiological diagnosis is essential to improve effective therapy delivery to affected individuals, preventing adverse outcomes and reducing antimicrobial resistance. METHODS We conducted a cross-sectional study of patients with suspected VAP and COVID-19, evaluating the diagnostic performance of the BioFire® FilmArray® Pneumonia Panel (FA-PP). Respiratory secretion samples underwent standard microbiological culture and FA-PP assays, and the results were compared. RESULTS We included 252 samples. The traditional culture method detected 141 microorganisms, and FA-PP detected 277, resulting in a sensitivity of 95% and specificity of 60%, with a positive predictive value of 68% and negative predictive value of 93%. In samples with high levels of genetic material (> 10^5 copies/mL), the panel had a sensitivity of 94% and specificity of 86%. In addition, 40% of the culture-negative samples had positive FA-PP® results, of which 35% had > 10^5 copies/mL of genetic material. The most prevalent bacteria were Gram-negative bacilli, followed by Gram-positive cocci. The panel identified 98 genes associated with antimicrobial resistance, predominantly extended-spectrum beta-lactamases (28%). CONCLUSION The FA-PP is a sensitive assay for identifying bacteria causing VAP in patients with COVID-19, with a greater capacity to detect bacteria than the conventional method. The timely microbiological recognition offered by this panel could lead to optimized decision-making processes, earlier tailored treatment initiation, and improved antibiotic stewardship practices.
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Affiliation(s)
- Gabriel Cojuc-Konigsberg
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
- Health Sciences Faculty, Universidad Anahuac Mexico, Mexico City, Mexico
| | - Alberto Moscona-Nissan
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | - Alberto Guijosa
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | | | - María E Jiménez Martínez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Mario A Mújica Sánchez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Martha A Durán Barrón
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Karen Villarreal Gómez
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | | | - Montserrat Ordóñez-Oviedo
- School of Medicine, Universidad Panamericana, Insurgentes Mixcoac, Donatello 59, 03920, Mexico City, Mexico
| | - Grecia Deloya Brito
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Eduardo Becerril Vargas
- Clinical Microbiology Laboratory, National Institute of Respiratory Diseases, Mexico City, Mexico.
- Health Sciences Faculty, Universidad Anahuac Mexico, Mexico City, Mexico.
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Puljko A, Rozman SD, Barišić I, Maravić A, Jelić M, Babić I, Milaković M, Petrić I, Udiković-Kolić N. Resistance to critically important antibiotics in hospital wastewater from the largest Croatian city. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161805. [PMID: 36708818 DOI: 10.1016/j.scitotenv.2023.161805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The emergence of extended-spectrum β-lactamase (ESBL)- and especially carbapenemases in Enterobacterales has led to limited therapeutic options. Therefore, it is critical to fully understand all potential routes of transmission, especially in high-risk sources such as hospital wastewater. This study aimed to quantify four enteric opportunistic pathogens (EOPs), total, ESBL- and carbapenem-resistant coliforms and their corresponding resistance genes (two ESBL and five carbapenemase genes) and to characterize enterobacterial isolates from hospital wastewater from two large hospitals in Zagreb over two seasons. Culturing revealed similar average levels of total and carbapenem-resistant coliforms (3.4 × 104 CFU/mL), and 10-fold lower levels of presumptive ESBL coliforms (3 × 103 CFU/mL). Real-time PCR revealed the highest E. coli levels among EOPs (105 cell equivalents/mL) and the highest levels of the blaKPC gene (up to 10-1 gene copies/16S copies) among all resistance genes examined. Of the 69 ESBL- and 90 carbapenemase-producing Enterobacterales (CPE) isolates from hospital wastewater, all were multidrug-resistant and most were identified as Escherichia coli, Citrobacter, Enterobacter, and Klebsiella. Among ESBL isolates, blaCTX-M-15 was the most prevalent ESBL gene, whereas in CPE isolates, blaKPC-2 and blaNDM-1 were the most frequently detected CP genes, followed by blaOXA-48. Molecular epidemiology using PFGE, MLST and whole-genome sequencing (WGS) revealed that clinically relevant variants such as E. coli ST131 (blaCTX-M-15/blaTEM-116) and ST541 (blaKPC-2), K. pneumoniae ST101 (blaOXA-48/blaNDM-1), and Enterobacter cloacae complex ST277 (blaKPC-2/blaNDM-1) were among the most frequently detected clone types. WGS also revealed a diverse range of resistance genes and plasmids in these and other isolates, as well as transposons and insertion sequences in the flanking regions of the blaCTX-M, blaOXA-48, and blaKPC-2 genes, suggesting the potential for mobilization. We conclude that hospital wastewater is a potential secondary reservoir of clinically important pathogens and resistance genes and therefore requires effective pretreatment before discharge to the municipal sewer system.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210 Vienna, Austria
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000 Split, Croatia
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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Gadsby NJ, Musher DM. The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures. Clin Microbiol Rev 2022; 35:e0001522. [PMID: 36165783 PMCID: PMC9769922 DOI: 10.1128/cmr.00015-22] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Enterobacteriaceae, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying Legionella and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.
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Affiliation(s)
- Naomi J. Gadsby
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Daniel M. Musher
- Michael E. DeBakey Veterans Administration Medical Center, Houston, Texas, USA
- Baylor College of Medicine, Houston, Texas, USA
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Taddei L, Malvisi L, Hui DS, Malvaux L, Samoro RZ, Haak Lee S, Cheong Yeung Y, Liu YC, Kumar Arora A. Airway pathogens detected in stable and exacerbated COPD in patients in Asia-Pacific. ERJ Open Res 2022; 8:00057-2022. [PMID: 36171985 PMCID: PMC9511156 DOI: 10.1183/23120541.00057-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/10/2022] [Indexed: 11/11/2022] Open
Abstract
Background The burden of chronic obstructive pulmonary disease (COPD) in the Asia-Pacific region is projected to increase. Data from other regions show bacterial and viral infections can trigger acute exacerbations of COPD (AECOPD). Methods This 1-year prospective epidemiological study (ClinicalTrials.gov identifier: NCT03151395) of patients with moderate to very severe COPD in Hong Kong, the Philippines, South Korea and Taiwan assessed the prevalence in sputum samples (by culture and PCR) of bacterial and viral pathogens during stable COPD and AECOPD. The odds of experiencing an exacerbation was evaluated for pathogen presence, acquisition and apparition. Health-related quality of life (HRQOL) was assessed. Results 197 patients provided 983 sputum samples, with 226 provided during exacerbation episodes. The mean yearly AECOPD incidence rate was 1.27 per patient. The most prevalent bacteria by PCR at exacerbation were Haemophilus influenzae (Hi) and Moraxella catarrhalis (Mcat); Mcat prevalence was higher at exacerbation than at stable state. Virus prevalence was low, other than for human rhinovirus (HRV) (8.1%, stable state; 16.6%, exacerbation). The odds ratio (95% CI) for an exacerbation (versus stable state) was statistically significant for the presence, acquisition and apparition of Hi (2.20, 1.26–3.89; 2.43, 1.11–5.35; 2.32, 1.20–4.46, respectively), Mcat (2.24, 1.30–3.88; 5.47, 2.16–13.86; 3.45, 1.71–6.98, respectively) and HRV (2.12, 1.15–3.91; 2.22, 1.09–4.54; 2.09, 1.11–3.91, respectively). HRQOL deteriorated according to the number of exacerbations experienced. Conclusion In patients with COPD in the Asia-Pacific region, the presence of Hi, Mcat or HRV in sputum samples significantly increased the odds of an exacerbation, providing further evidence of potential roles in triggering AECOPD. The presence of Haemophilus influenzae, Moraxella catarrhalis or human rhinovirus in sputum samples significantly increases the odds of an exacerbation, as opposed to being in stable state, in COPDhttps://bit.ly/39vI3XU
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14
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Zhao MC, Jiang Y, Li GX, Tie YQ, Zheng YH, Li JF, Zhang WC, Duan SX, Zhai Y, Li YL, Zhang DJ, Zeng XP, Wu Y, Guo YH, Feng ZS. Simultaneous detection of 9 respiratory pathogens using a newly developed multiplex real-time PCR panel based on an automatic molecular detection and analysis system. Diagn Microbiol Infect Dis 2022; 104:115801. [DOI: 10.1016/j.diagmicrobio.2022.115801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/18/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
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15
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Zhuo X, Zhao J, Wang L, Sun B, Sun L, Wang C, Li B, Fan Y, Liu Y, Cao B. Development and evaluation of a multiplex quantitative polymerase chain reaction assay for detecting bacteria associated with lower respiratory tract infection. Int J Infect Dis 2022; 122:202-211. [PMID: 35644352 DOI: 10.1016/j.ijid.2022.05.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES This study aimed to establish a multiplex quantitative polymerase chain reaction (MQ-PCR) assay for 12 bacterial pathogens found in lower respiratory tract infection (LRTI) and to evaluate its performance in a cohort of 211 patients with LRTI. METHODS The study was divided into two stages: a pilot study to establish the methodology and a clinical validation study to evaluate its performance. In the pilot study, we established the MQ-PCR and analyzed its performance regarding limits of detection, reproducibility, specificity, and efficiency. In the clinical validation study, we obtained 211 sputum and/or bronchoalveolar lavage fluid (BALF) samples and detected pathogens by MQ-PCR. The MQ-PCR time was 3 h from sample collection to complete pathogen detection. RESULTS The limit of detection was 1000 copies/ml, and the maximum efficiency was >95%. When cutoffs of ≥105 copies/ml in sputum and ≥104 copies/ml in BALF were applied, the sensitivity, specificity, and positive and negative predictive values of the MQ-PCR were 77% (95% confidence interval [CI] 67-88%), 94% (95% CI 93-95%), 25% (95% CI 19-31%), and 99% (95% CI 99-100%), respectively. CONCLUSIONS This study demonstrates that the new MQ-PCR assay is time-saving, more effective and sensitive, and brings us closer to mainstream adoption of quantitative molecular detection of bacteria.
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Affiliation(s)
- Xianxia Zhuo
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Lei Wang
- Beijing Applied Biological Technologies Co., Ltd
| | - Bin Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Lanhua Sun
- Beijing Applied Biological Technologies Co., Ltd
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Binbin Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Yingmei Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China; Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China; Institute of Respiratory Medicine, Chinese Academy of Medical Science; National Clinical Research Center of Respiratory Diseases, Beijing, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China.
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Ghorbani J, Hashemi FB, Jabalameli F, Emaneini M, Beigverdi R. Multiplex detection of five common respiratory pathogens from bronchoalveolar lavages using high resolution melting curve analysis. BMC Microbiol 2022; 22:141. [PMID: 35590256 PMCID: PMC9118692 DOI: 10.1186/s12866-022-02558-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Background The study describes the application of the multiplex high-resolution melting curve (MHRM) assay for the simultaneous detection of five common bacterial pathogens (Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii and Escherichia coli) directly from bronchoalveolar lavage samples. Results Our MHRM assay successfully identified all five respiratory pathogens in less than 5 h, with five separate melting curves with specific melt peak temperatures (Tm). The different Tm were characterized by peaks of 78.1 ± 0.4 °C for S. aureus, 83.3 ± 0.1 °C for A. baumannii, 86.7 ± 0.2 °C for E. coli, 90.5 ± 0.1 °C for K. pneumoniae, 94.5 ± 0.2 °C for P. aeruginosa. The overall sensitivity and specificity of MHRM were 100% and 88.8–100%, respectively. Conclusions Our MHRM assay offers a simple and fast alternative to culture approach for simultaneous detection of five major bacterial lower respiratory tract infection pathogens. Utilization of this assay can help clinicians initiate prompt and appropriate antimicrobial treatment, towards reducing the morbidity and mortality of severe respiratory infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02558-2.
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Affiliation(s)
- Jaber Ghorbani
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Farhad Bonakdar Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran.,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran. .,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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Shoar S, Musher DM. The white blood cell response in sputum in viral and bacterial pneumonias. Open Forum Infect Dis 2022; 9:ofac189. [PMID: 35794935 PMCID: PMC9251662 DOI: 10.1093/ofid/ofac189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/09/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Saeed Shoar
- Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Daniel M. Musher
- Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
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18
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Puljko A, Milaković M, Križanović S, Kosić-Vukšić J, Babić I, Petrić I, Maravić A, Jelić M, Udiković-Kolić N. Prevalence of enteric opportunistic pathogens and extended-spectrum cephalosporin- and carbapenem-resistant coliforms and genes in wastewater from municipal wastewater treatment plants in Croatia. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128155. [PMID: 34991006 DOI: 10.1016/j.jhazmat.2021.128155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/29/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales are a critical global health problem and wastewater treatment plants (WWTPs) can promote their spread into the environment; yet their efficacy is not well characterized. Here, we have used conventional culturing to monitor coliform bacteria and quantitative PCR to monitor 2 ESBL and 5 carbapenemase (CP) genes and 4 enteric opportunistic pathogens (EOPs) in the influent and effluent of 7 Croatian WWTPs in two seasons. In general, levels of total, cefotaxime- and carbapenem-resistant coliforms were significantly reduced but not eliminated by conventional treatment in most WWTPs. Most WWTPs efficiently removed EOPs such as K. pneumoniae and A. baumannii, while E. coli and Enterococcus spp. were reduced but still present in relatively high concentrations in the effluent. ESBL genes (blaTEM and blaCTX-M-32) were only slightly reduced or enriched after treatment. CP genes, blaKPC-3, blaNDM and blaOXA-48-like, were sporadically detected, while blaIMP and blaVIM were frequently enriched during treatment and correlated with plant size, number or size of hospitals in the catchment area, and COD effluent concentration. Our results suggest that improvements in wastewater treatment technologies are needed to minimize the risk of environmental contamination with top priority EOPs and ARGs and the resulting public health.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 000 Zagreb, Croatia
| | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 000 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 000 Zagreb, Croatia
| | - Josipa Kosić-Vukšić
- Andrija Štampar Teaching Institute of Public Health, Mirogojska cesta 16, 10 000 Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 000 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 000 Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000 Split, Croatia
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 000 Zagreb, Croatia.
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Schoonbroodt S, Ichanté JL, Boffé S, Devos N, Devaster JM, Taddei L, Rondini S, Arora AK, Pascal T, Malvaux L. Real-time PCR has advantages over culture-based methods in identifying major airway bacterial pathogens in chronic obstructive pulmonary disease: Results from three clinical studies in Europe and North America. Front Microbiol 2022; 13:1098133. [PMID: 36909845 PMCID: PMC10000296 DOI: 10.3389/fmicb.2022.1098133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/29/2022] [Indexed: 03/14/2023] Open
Abstract
Introduction We compared the performance of real-time PCR with culture-based methods for identifying bacteria in sputum samples from patients with chronic obstructive pulmonary disease (COPD) in three studies. Methods This was an exploratory analysis of sputum samples collected during an observational study of 127 patients (AERIS; NCT01360398), phase 2 study of 145 patients (NTHI-004; NCT02075541), and phase 2b study of 606 patients (NTHI-MCAT-002; NCT03281876). Bacteria were identified by culture-based microbiological methods in local laboratories using fresh samples or by real-time PCR in a central laboratory using frozen samples. Haemophilus influenzae positivity with culture was differentiated from H. haemolyticus positivity by microarray analysis or PCR. The feasibility of bacterial detection by culture-based methods on previously frozen samples was also examined in the NTHI-004 study. Results Bacterial detection results from both culture-based and PCR assays were available from 2,293 samples from AERIS, 974 from the NTHI-004 study, and 1736 from the NTHI-MCAT-002 study. Quantitative real-time PCR (qPCR) showed higher positivity rates than culture for H. influenzae (percentages for each study: 43.4% versus 26.2%, 47.1% versus 23.6%, 32.7% versus 10.4%) and Moraxella catarrhalis (12.9% versus 6.3%, 19.0% versus 6.0%, 15.5% versus 4.1%). In the NTHI-004 and NTHI-MCAT-002 studies, positivity rates were higher with qPCR for Streptococcus pneumoniae (15.6% versus 6.1%, 15.5% versus 3.8%); in AERIS, a lower rate with qPCR than with culture (11.0% versus 17.4%) was explained by misidentification of S. pseudopneumoniae/mitis isolates via conventional microbiological methods. Concordance analysis showed lowest overall agreement for H. influenzae (82.0%, 75.6%, 77.6%), due mainly to culture-negative/qPCR-positive samples, indicating lower sensitivity of the culture-based methods. The lowest positive agreement (culture-positive/qPCR-positive samples) was observed for S. pneumoniae (35.1%, 71.2%, 71.2%). Bacterial load values for each species showed a proportion of culture-negative samples with a load detected by qPCR; for some samples, the loads were in line with those observed in culture-positive samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples. Discussion Real-time PCR on frozen sputum samples has enhanced sensitivity and specificity over culture-based methods, supporting its use for the identification of common respiratory bacterial species in patients with COPD.
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Terranova L, Risé P, Gramegna A, Pinna C, Agostoni C, Syrén ML, Turolo S, Marchisio P, Amati F, Aliberti S, Sala A, Blasi F. Pro-resolving and pro-inflammatory fatty acid-derived mediators in sputum of stable state bronchiectasis patients. Respir Res 2022; 23:363. [PMID: 36539829 PMCID: PMC9764713 DOI: 10.1186/s12931-022-02301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Bronchiectasis is characterized by neutrophilic inflammation and frequent exacerbations often associated with infections. Lipid mediators play critical roles in the inflammatory response, and the balance between anti-inflammatory and pro-inflammatory mediators could drive to chronic inflammation. The aim of this study was to evaluate the metabolites of docosahexaenoic acid and arachidonic acid in sputum of adults with bronchiectasis defining their associations with clinical data, bacterial load and neutrophil elastase. METHODS An observational, cross-sectional study was conducted at the bronchiectasis program of the Policlinico Hospital in Milan, Italy, where patients were enrolled. Active neutrophil elastase was measured by enzyme-linked immunosorbent assay, pro-resolving and pro-inflammatory fatty acid-derived mediators were evaluated by mass spectrometry and respiratory pathogens were assessed by real-time PCR. Analysis were performed on sputum collected during stable state and clinical data were also collected. RESULTS Levels of pro-inflammatory mediators derived from arachidonic acid metabolism showed association with neutrophil elastase, were proportional to Pseudomonas aeruginosa identifications and were linked with radiological gravity index, while the concentrations of pro-resolution mediators derived from docosahexaenoic acid were associated with a better health status, highlighted by the inverse correlation with radiological gravity index, bacterial infections and sputum volume production. CONCLUSION Pro-inflammatory mediators derived from FA metabolisms are associated with severity of bronchiectasis while DHA-derived metabolites are inversely associated with severity of the disease, which may be used for personized treatment of bronchiectasis.
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Affiliation(s)
- Leonardo Terranova
- grid.414818.00000 0004 1757 8749Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Patrizia Risé
- grid.4708.b0000 0004 1757 2822Department of Pharmaceutical Sciences-DISFARM, University of Milan, 20122 Milan, Italy
| | - Andrea Gramegna
- grid.414818.00000 0004 1757 8749Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Christian Pinna
- grid.4708.b0000 0004 1757 2822Department of Pharmaceutical Sciences-DISFARM, University of Milan, 20122 Milan, Italy
| | - Carlo Agostoni
- grid.414818.00000 0004 1757 8749Pediatric Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Marie-Louise Syrén
- grid.4708.b0000 0004 1757 2822Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Stefano Turolo
- grid.414818.00000 0004 1757 8749Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Paola Marchisio
- grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy ,grid.414818.00000 0004 1757 8749Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Francesco Amati
- grid.452490.eDepartment of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy ,grid.417728.f0000 0004 1756 8807Respiratory Unit, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Stefano Aliberti
- grid.452490.eDepartment of Biomedical Sciences, Humanitas University, 20072 Pieve Emanuele, Italy ,grid.417728.f0000 0004 1756 8807Respiratory Unit, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Angelo Sala
- grid.4708.b0000 0004 1757 2822Department of Pharmaceutical Sciences-DISFARM, University of Milan, 20122 Milan, Italy
| | - Francesco Blasi
- grid.414818.00000 0004 1757 8749Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
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21
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Lin WH, Chiu HC, Chen KF, Tsao KC, Chen YY, Li TH, Huang YC, Hsieh YC. Molecular detection of respiratory pathogens in community-acquired pneumonia involving adults. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 55:829-837. [PMID: 34969624 DOI: 10.1016/j.jmii.2021.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 11/10/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Community-acquired pneumonia (CAP) causes substantial morbidity and mortality in adults worldwide. The etiology of CAP often remains uncertain, and therapy is empirical. Thus, there is still room for improvement in the diagnosis of pneumonia. METHODS Adults aged >20 years who presented at the outpatient or emergency departments of Linkou and Keelung Chang Gung Memorial Hospital with CAP were prospectively included between November 2016 and December 2018. We collected respiratory specimens for culture and molecular testing and calculated the incidence rates of CAP according to pathogens. RESULTS Of 212 hospitalized adult patients with CAP, 69.3% were male, and the median age of the patients was 67.8 years. Bacterial pathogens were detected in 106 (50%) patients, viruses in 77 (36.3%), and fungal pathogens in 1 patient (0.5%). The overall detection rate (culture and molecular testing method) was 70.7% (n = 150). Traditional microbial culture yielded positive results in 36.7% (n = 78), molecular testing in 61.3% (n = 130). The most common pathogens were influenza (16.1%), followed by Klebsiella pneumoniae (14.1%), Pseudomonas aeruginosa (13.6%), human rhinovirus (11.8%), and Streptococcus pneumoniae (9.9%). Multiple pathogen co-infections accounted for 28.7% (n = 61), of which co-infection with K. pneumoniae and human rhinovirus comprised the largest proportion. CONCLUSIONS Molecular diagnostic testing could detect 23.6% more pathogens than traditional culture techniques. However, despite the current diagnostic tests, there is still the possibility that no pathogen was detected.
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Affiliation(s)
- Wei-Hsuan Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Han-Cheng Chiu
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Kuan-Fu Chen
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan; Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Ting-Hsuan Li
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Yhu-Chering Huang
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Taipei, Taoyuan, Taiwan.
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Taipei, Taoyuan, Taiwan.
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22
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Paukner S, Goldberg L, Alexander E, Das AF, Heinrich S, Patel P, Moran GJ, Sandrock C, File TM, Vidal JE, Waites KB, Gelone SP, Schranz J. Pooled Microbiological Findings and Efficacy Outcomes by Pathogen in Adults With Community-Acquired Bacterial Pneumonia from the Lefamulin Evaluation Against Pneumonia (LEAP) 1 and LEAP 2 Phase 3 Trials of Lefamulin Versus Moxifloxacin. J Glob Antimicrob Resist 2021; 29:434-443. [PMID: 34788694 DOI: 10.1016/j.jgar.2021.10.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Lefamulin, a pleuromutilin antibiotic approved for community-acquired bacterial pneumonia (CABP), was evaluated for microbiological efficacy in a prespecified pooled analysis of LEAP 1 and 2 phase 3 clinical trial data in patients with CABP. METHODS In LEAP 1, adults (Pneumonia Outcomes Research Team [PORT] risk class III‒V) received intravenous (IV) lefamulin 150 mg every 12 hours (q12h; 5‒7 days) or moxifloxacin 400 mg every 24 hours (q24h; 7 days), with optional IV-to-oral switch. In LEAP 2, adults (PORT II‒IV) received oral lefamulin 600 mg q12h (5 days) or moxifloxacin 400 mg q24h (7 days). Primary outcomes were early clinical response (ECR) 96±24 hours after treatment start and investigator assessment of clinical response (IACR) 5‒10 days after last dose. Secondary outcomes included ECR and IACR in patients with a baseline CABP pathogen (detected via culture, urinary antigen test, serology, and/or real-time PCR). RESULTS Baseline CABP pathogens were detected in 709/1289 patients (55.0% [microbiological intent-to-treat population]). The most frequently identified pathogens in this population were Streptococcus pneumoniae (61.9% of patients) and Haemophilus influenzae (29.9%); 25.1% had atypical pathogens and 33.1% had polymicrobial infections. Pathogens were identified most frequently by PCR from sputum, followed by culture from respiratory specimens. In patients with baseline CABP pathogens, ECR rates were 89.3% (lefamulin) and 93.0% (moxifloxacin); IACR success rates were 83.2% and 86.7%, respectively. Results were consistent across CABP pathogens, including drug-resistant isolates and polymicrobial infections. CONCLUSIONS Lefamulin is a valuable IV and oral monotherapy option for empiric and directed CABP treatment in adults.
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Affiliation(s)
| | - Lisa Goldberg
- Nabriva Therapeutics US, Inc., Fort Washington, PA, USA
| | | | | | | | - Pritty Patel
- Covance Central Laboratory Services, Indianapolis, IN, USA
| | - Gregory J Moran
- Department of Emergency Medicine & Division of Infectious Diseases, Olive View-UCLA Medical Center, Los Angeles, CA, USA
| | - Christian Sandrock
- Department of Internal Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Thomas M File
- Infectious Disease Division, Summa Health, Akron, OH, USA
| | - Jorge E Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Ken B Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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23
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Voiriot G, Fartoukh M, Durand-Zaleski I, Berard L, Rousseau A, Armand-Lefevre L, Verdet C, Argaud L, Klouche K, Megarbane B, Patrier J, Richard JC, Reignier J, Schwebel C, Souweine B, Tandjaoui-Lambiotte Y, Simon T, Timsit JF. Combined use of a broad-panel respiratory multiplex PCR and procalcitonin to reduce duration of antibiotics exposure in patients with severe community-acquired pneumonia (MULTI-CAP): a multicentre, parallel-group, open-label, individual randomised trial conducted in French intensive care units. BMJ Open 2021; 11:e048187. [PMID: 34408046 PMCID: PMC8375718 DOI: 10.1136/bmjopen-2020-048187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION At the time of the worrying emergence and spread of bacterial resistance, reducing the selection pressure by reducing the exposure to antibiotics in patients with community-acquired pneumonia (CAP) is a public health issue. In this context, the combined use of molecular tests and biomarkers for guiding antibiotics discontinuation is attractive. Therefore, we have designed a trial comparing an integrated approach of diagnosis and treatment of severe CAP to usual care. METHODS AND ANALYSIS The multiplex PCR and procalcitonin to reduce duration of antibiotics exposure in patients with severe-CAP (MULTI-CAP) trial is a multicentre (n=20), parallel-group, superiority, open-label, randomised trial. Patients are included if adult admitted to intensive care unit for a CAP. Diagnosis of pneumonia is based on clinical criteria and a newly appeared parenchymal infiltrate. Immunocompromised patients are excluded. Subjects are randomised (1:1 ratio) to either the intervention arm (experimental strategy) or the control arm (usual strategy). In the intervention arm, the microbiological diagnosis combines a respiratory multiplex PCR (mPCR) and conventional microbiological investigations. An algorithm of early antibiotic de-escalation or discontinuation is recommended, based on mPCR results and the procalcitonin value. In the control arm, only conventional microbiological investigations are performed and antibiotics de-escalation remains at the clinician's discretion. The primary endpoint is the number of days alive without any antibiotic from the randomisation to day 28. Based on our hypothesis of 2 days gain in the intervention arm, we aim to enrol a total of 450 patients over a 30-month period. ETHICS AND DISSEMINATION The MULTI-CAP trial is conducted according to the principles of the Declaration of Helsinki, is registered in Clinical Trials and has been approved by the Committee for Protection of Persons and the National French Drug Safety Agency. Written informed consents are obtained from all the patients (or representatives). The results will be disseminated through educational institutions, submitted to peer-reviewed journals for publication and presented at medical congresses. TRIAL REGISTRATION NUMBER NCT03452826; Pre-results.
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Affiliation(s)
- Guillaume Voiriot
- Service de Médecine Intensive Réanimation, Assistance Publique-Hopitaux de Paris, Paris, France
| | - Muriel Fartoukh
- Service de Médecine Intensive Réanimation, Assistance Publique-Hopitaux de Paris, Paris, France
| | | | - Laurence Berard
- Unité de Recherche Clinique de l'Est Parisien, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
| | - Alexandra Rousseau
- Unité de Recherche Clinique de l'Est Parisien, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
| | - Laurence Armand-Lefevre
- Département de Microbiologie, Hôpital Bichat, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
| | - Charlotte Verdet
- Département de Microbiologie, Hôpital Saint-Antoine, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
| | - Laurent Argaud
- Service de Médecine Intensive-Réanimation, Hôpital Edouard Herriot, Université de Lyon, Lyon, France
| | - Kada Klouche
- Intensive Care Medicine Department, Universite de Montpellier, Montpellier, France
| | - Bruno Megarbane
- Service de Médecine Intensive Réanimation, Hôpital Lariboisière, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
| | - Juliette Patrier
- Service de Réanimation Infectieuse, Hôpital Bichat, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
| | - Jean-Christophe Richard
- Service de Médecine Intensive Réanimation, Hôpital de la Croix-Rousse, Université de Lyon, Lyon, France
| | - Jean Reignier
- Médecine intensive réanimation, CHU Nantes, Nantes, Pays de la Loire, France
| | - Carole Schwebel
- Service de Médecine Intensive Réanimation, CHU Grenoble Alpes, Grenoble, Auvergne-Rhone-Alpes, France
| | - Bertrand Souweine
- Medical Intensive Care Unit, CHU Gabriel-Montpied, Clermont-Ferrand, France
| | - Yacine Tandjaoui-Lambiotte
- Service de Réanimation médico-chirurgicale, Hôpital Avicennes, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
| | - Tabassome Simon
- Clinical Research Platform (URC-CRB-CRC), Assistance Publique-Hôpitaux de Paris, Saint Antoine Hospital, Paris, France
- Clinical Pharmacology-Research Platform, Université Pierre et Marie Curie, Paris, France
| | - Jean-François Timsit
- Service de Réanimation Infectieuse, Hôpital Bichat, Assistance Publique-Hopitaux de Paris, Paris, Île-de-France, France
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Sun L, Zhang C, An S, Chen X, Li Y, Xiu L, Xu B, Xie Z, Peng J. Comprehensive Description of Pathogens and Antibiotic Treatment Guidance in Children With Community-Acquired Pneumonia Using Combined Mass Spectrometry Methods. Front Cell Infect Microbiol 2021; 11:695134. [PMID: 34368015 PMCID: PMC8335481 DOI: 10.3389/fcimb.2021.695134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/15/2021] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to evaluate the value of molecular methods in the management of community-acquired pneumonia (CAP) in children. Previously developed mass spectrometry (MS)-based methods combined with quantitative real-time PCR (combined-MS methods) were used to describe the aetiology and evaluate antibiotic therapy in the enrolled children. Sputum collected from 302 children hospitalized with CAP were analyzed using the combined-MS methods, which can detect 19 viruses and 12 bacteria related to CAP. Based on the results, appropriate antibiotics were determined using national guidelines and compared with the initial empirical therapies. Respiratory pathogens were identified in 84.4% of the patients (255/302). Co-infection was the predominant infection pattern (51.7%, 156/302) and was primarily a bacterial-viral mixed infection (36.8%, 111/302). Compared with that using culture-based methods, the identification rate for bacteria using the combined-MS methods (61.8%, 126/204) increased by 28.5% (p <0.001). Based on the results of the combined-MS methods, the initial antibiotic treatment of 235 patients was not optimal, which mostly required switching to β-lactam/β-lactamase inhibitor combinations or reducing unnecessary macrolide treatments. Moreover, using the combined-MS methods to guide antibiotic therapy showed potential to decrease the length of stay in children with severe CAP. For children with CAP, quantitative molecular testing on sputum can serve as an important complement to traditional culture methods. Early aetiology elucidated using molecular testing can help guide the antibiotic therapy.
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Affiliation(s)
- Liying Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chi Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuhua An
- Department of Respiratory Medicine, Hebei Children's Hospital, Hebei Medical University, Shijiazhuang, China
| | - Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yamei Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Leshan Xiu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoping Xu
- National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Respiratory Department, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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25
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Lim HJ, Kang ER, Park MY, Kim BK, Kim MJ, Jung S, Roh KH, Sung N, Yang JH, Lee MW, Lee SH, Yang YJ. Development of a multiplex real-time PCR assay for the simultaneous detection of four bacterial pathogens causing pneumonia. PLoS One 2021; 16:e0253402. [PMID: 34138947 PMCID: PMC8211157 DOI: 10.1371/journal.pone.0253402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classification of clinical symptoms and diagnostic microbiology are essential to effectively employ antimicrobial therapy for lower respiratory tract infections (LRTIs) in a timely manner. Empirical antibiotic treatment without microbial identification hinders the selective use of narrow-spectrum antibiotics and effective patient treatment. Thus, the development of rapid and accurate diagnostic procedures that can be readily adopted by the clinic is necessary to minimize non-essential or excessive use of antibiotics and accelerate patient recovery from LRTI-induced damage. We developed and validated a multiplex real-time polymerase chain reaction (mRT-PCR) assay with good analytical performance and high specificity to simultaneously detect four bacterial pathogens causing pneumonia: Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Moraxella catarrhalis. The analytical performance of mRT-PCR against target pathogens was evaluated by the limit of detection (LOD), specificity, and repeatability. Two hundred and ten clinical specimens from pneumonia patients were processed using an automatic nucleic acid extraction system for the “respiratory bacteria four” (RB4) mRT-PCR assay, and the results were directly compared to references from bacterial culture and/or Sanger sequencing. The RB4 mRT-PCR assay detected all target pathogens from sputum specimens with a coefficient of variation ranging from 0.29 to 1.71 and conservative LOD of DNA corresponding to 5 × 102 copies/reaction. The concordance of the assay with reference-positive specimens was 100%, and additional bacterial infections were detected from reference-negative specimens. Overall, the RB4 mRT-PCR assay showed a more rapid turnaround time and higher performance that those of reference assays. The RB4 mRT-PCR assay is a high-throughput and reliable tool that assists decision-making assessment and outperforms other standard methods. This tool supports patient management by considerably reducing the inappropriate use of antibiotics.
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Affiliation(s)
- Ho Jae Lim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea
| | - Eun-Rim Kang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Young Park
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Bo Kyung Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Jin Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Sunkyung Jung
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Gyeonggi, Republic of Korea
| | - Nackmoon Sung
- Clinical Research Institute, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS) and Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Sun-Hwa Lee
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Yong-Jin Yang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- * E-mail:
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Third-Generation Anti-CD47-Specific CAR-T Cells Effectively Kill Cancer Cells and Reduce the Genes Expression in Lung Cancer Cell Metastasis. J Immunol Res 2021; 2021:5575260. [PMID: 34189144 PMCID: PMC8192203 DOI: 10.1155/2021/5575260] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/09/2021] [Accepted: 05/09/2021] [Indexed: 02/04/2023] Open
Abstract
CD47 is a cell surface glycoprotein molecule, belonging to the immunoglobulin superfamily, binding to various proteins including integrins, thrombospondin-1, and signal regulatory protein α (SIRPα). CD47 is an important tumor antigen for the development and progression of various cancers. This study designed the chimeric antigen receptor T-cell (CAR-T) to bind to the CD47 to inhibit the expression of CD47. We used the complementarity-determining regions (CDRs) of the B6H12 mouse antibody grafted onto the IgG1 framework to create the humanized single-chain variable fragment (scFv) with linker (G4S)x3. scFv was used to design the chimeric antigen receptor with the structure CD8signal-CD47scFv-CD8a hinge-CD4TM-CD28-41BB-CD3ζ, which was then transformed into T lymphocytes by the lentivirus to create third generation of CAR-T. Results revealed that the new CAR-T cells efficiently killed A549 cancer cells. CAR-T inhibited the expression of genes involved in metastasis and invasion of cells A549 including beta actin, calreticulin, and cyclooxygenase 2 at mRNA levels.
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Malvisi L, Taddei L, Yarraguntla A, Wilkinson TMA, Arora AK. Sputum sample positivity for Haemophilus influenzae or Moraxella catarrhalis in acute exacerbations of chronic obstructive pulmonary disease: evaluation of association with positivity at earlier stable disease timepoints. Respir Res 2021; 22:67. [PMID: 33627095 PMCID: PMC7903661 DOI: 10.1186/s12931-021-01653-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/07/2021] [Indexed: 12/04/2022] Open
Abstract
Background Infection with Haemophilus influenzae (Hi) or Moraxella catarrhalis (Mcat) is a risk factor for exacerbation in chronic obstructive pulmonary disease (COPD). The ability to predict Hi- or Mcat-associated exacerbations may be useful for interventions developed to reduce exacerbation frequency. Methods In a COPD observational study, sputum samples were collected at monthly stable-state visits and at exacerbation during two years of follow-up. Bacterial species (Hi, Mcat) were identified by culture and quantitative PCR assay. Post-hoc analyses were conducted to assess: (1) first Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at the screening visit (stable-state timepoint); (2) first Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at stable timepoints within previous 90 days; (3) second Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at stable timepoints within previous 90 days. Percentages and risk ratios (RRs) with 95% confidence intervals were calculated. Results PCR results for analyses 1, 2 and 3 (samples from 84, 88 and 83 subjects, respectively) showed that the risk of an Hi- or Mcat-positive exacerbation is significantly higher if sputum sample was Hi- or Mcat-positive than if Hi- or Mcat-negative at previous stable timepoints (apart from Mcat in analysis 3); RRs ranged from 2.1 to 3.2 for Hi and 1.9 to 2.6 for Mcat.For all analyses, the percentage of Hi- or Mcat-positive exacerbations given previous Hi- or Mcat-positive stable timepoints was higher than the percentage of Hi- or Mcat-positive exacerbations if Hi- or Mcat-negative at previous stable timepoints. Percentage of Hi- or Mcat-positive exacerbations given previous Hi- or Mcat-negative stable timepoints was 26.3%–37.0% for Hi and 17.6%–19.7% for Mcat. Conclusions Presence of Hi or Mcat at a stable timepoint was associated with a higher risk of a subsequent Hi- or Mcat-associated exacerbation compared with earlier absence. However, a large percentage of Hi- or Mcat-associated exacerbations was not associated with Hi/Mcat detection at an earlier timepoint. This suggests that administration of an intervention to reduce these exacerbations should be independent of bacterial presence at baseline. Trial Registrationhttps://clinicaltrials.gov/; NCT01360398, registered May 25, 2011
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Affiliation(s)
| | | | | | - Tom M A Wilkinson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Southampton NIHR Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,Wessex Investigational Sciences Hub, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
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28
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Wang H, Gu J, Li X, van der Gaast-de Jongh CE, Wang W, He X, Xu Z, Yang Y, de Groot R, de Jonge MI, Zheng Y. Broad range detection of viral and bacterial pathogens in bronchoalveolar lavage fluid of children to identify the cause of lower respiratory tract infections. BMC Infect Dis 2021; 21:152. [PMID: 33546631 PMCID: PMC7864134 DOI: 10.1186/s12879-021-05834-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/22/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Knowledge on the etiology of LRTIs is essential for improvement of the clinical diagnosis and accurate treatment. Molecular detection methods were applied to identify a broad range of bacterial and viral pathogens in a large set of bronchial alveolar lavage (BAL) fluid samples. The patterns of detected pathogens were correlated to the clinical symptoms. METHODS BAL fluid samples and clinical data were collected from 573 hospitalized children between 1 month and 14 years of age with LRTIs, enrolled from January to December 2018. Pathogens were detected using standardized clinical diagnostics, with a sensitive, high-throughput GeXP-based multiplex PCR and with multiplex qPCR. Data were analyzed to describe the correlation between the severity of respiratory tract disease and the pathogens identified. RESULTS The pathogen detection rate with GeXP-based PCR and multiplex qPCR was significantly higher than by clinical routine diagnostics (76.09% VS 36.13%,χ2 = 8.191, P = 0.004). The most frequently detected pathogens in the BAL fluid were human adenovirus (HADV)(21.82%), Mycoplasma pneumoniae (20.24%), human rhinovirus (13.96%), Streptococcus pneumoniae (8.90%) and Haemophilus influenzae (8.90%). In 16.4% of the cases co-detection with two or three different pathogens was found. Viral detection rates declined with age, while atypical pathogen detection rates increased with age. Oxygen supply in the HADV and Influenza H1N1 infected patients was more frequent (49.43%) than in patients infected with other pathogens. CONCLUSION Broad range detection of viral and bacterial pathogens using molecular methods is a promising and implementable approach to improve clinical diagnosis and accurate treatment of LRTI in children.
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Affiliation(s)
- Heping Wang
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Philips van Leydenlaan 15, 6525 EX, Nijmegen, The Netherlands
| | - Jiali Gu
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Xiaonan Li
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Christa E van der Gaast-de Jongh
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Philips van Leydenlaan 15, 6525 EX, Nijmegen, The Netherlands
| | - Wenjian Wang
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Xuehui He
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Philips van Leydenlaan 15, 6525 EX, Nijmegen, The Netherlands
| | - Zhi Xu
- Ningbo Health Gene Technologies Co., Ltd., Ningbo, Zhejiang, China
| | - Yonghong Yang
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Ronald de Groot
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Philips van Leydenlaan 15, 6525 EX, Nijmegen, The Netherlands
| | - Marien I de Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud university medical center, Philips van Leydenlaan 15, 6525 EX, Nijmegen, The Netherlands.
| | - Yuejie Zheng
- Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China.
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29
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Messous S, Elargoubi A, Pillet S, Rajoharison A, Hoffmann J, Trabelsi I, Grissa MH, Boukef R, Beltaief K, Mastouri M, Paranhos-Baccalà G, Nouira S, Pozzetto B. Bacterial and Viral Infection in Patients Hospitalized for Acute Exacerbation of Chronic Obstructive Pulmonary Disease: Implication for Antimicrobial Management and Clinical Outcome. COPD 2020; 18:53-61. [PMID: 33353408 DOI: 10.1080/15412555.2020.1854210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Patients with chronic obstructive pulmonary disease (COPD) exhibit frequent acute exacerbations (AE). The objectives of this study were first to evaluate the prevalence of pathogens associated to these episodes by combining conventional bacteriology and multiplex viral and bacterial PCR assays in sputum specimens, and second to determine whether C-reactive protein (CRP) value and clinical outcome could be influenced by the type of microbial agent(s) recovered from these samples. A cohort of 84 Tunisian patients hospitalized at the emergency room for AECOPD was investigated prospectively for the semi-quantitative detection of bacteria by conventional culture (the threshold of positivity was of 107 CFU/ml) and for the detection of viral genome and DNA of atypical bacteria by quantitative PCR using two commercial multiplex respiratory kits (Seegene and Fast-track). The two kits exhibited very similar performances although the Seegene assay was a bit more sensitive. A large number and variety of pathogens were recovered from the sputum samples of these 84 patients, including 15 conventional bacteria, one Chlamydia pneumoniae and 63 respiratory viruses, the most prevalent being rhinoviruses (n = 33) and influenza viruses (n = 13). From complete results available for 74 patients, the presence of bacteria was significantly associated with risk of recurrence at 6 and 12 months post-infection. The combination of these different markers appears useful for delineating correctly the antimicrobial treatment and for initiating a long-term surveillance in those patients with high risk of recurrent exacerbation episodes. A prospective study is required for confirming the benefits of this strategy aimed at improving the stewardship of antibiotics.
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Affiliation(s)
- Salma Messous
- Research Laboratory (LR12SP18), University of Monastir, Monastir, Tunisia.,Microbiology Laboratory, Fattouma Bourguiba University Hospital of Monastir, Monastir, Tunisia
| | - Aida Elargoubi
- Microbiology Laboratory, Fattouma Bourguiba University Hospital of Monastir, Monastir, Tunisia
| | - Sylvie Pillet
- Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, and GIMAP group (EA 3064), Faculty of Medicine de Saint-Etienne, University of Lyon, Lyon, France
| | - Alain Rajoharison
- Laboratory of Emerging Pathogens, Mérieux Foundation, CIRI, Inserm U1111, Lyon, France
| | - Jonathan Hoffmann
- Laboratory of Emerging Pathogens, Mérieux Foundation, CIRI, Inserm U1111, Lyon, France
| | - Imen Trabelsi
- Research Laboratory (LR12SP18), University of Monastir, Monastir, Tunisia
| | - Mohamed Habib Grissa
- Research Laboratory (LR12SP18), University of Monastir, Monastir, Tunisia.,Department of Emergency, Fattouma Bourguiba University Hospital of Monastir, Monastir, Tunisia
| | - Riadh Boukef
- Research Laboratory (LR12SP18), University of Monastir, Monastir, Tunisia.,Department of Emergency, Sahloul University Hospital, Sousse, Tunisia
| | - Kaouther Beltaief
- Research Laboratory (LR12SP18), University of Monastir, Monastir, Tunisia.,Department of Emergency, Fattouma Bourguiba University Hospital of Monastir, Monastir, Tunisia
| | - Maha Mastouri
- Microbiology Laboratory, Fattouma Bourguiba University Hospital of Monastir, Monastir, Tunisia
| | | | - Semir Nouira
- Research Laboratory (LR12SP18), University of Monastir, Monastir, Tunisia.,Department of Emergency, Fattouma Bourguiba University Hospital of Monastir, Monastir, Tunisia
| | - Bruno Pozzetto
- Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, and GIMAP group (EA 3064), Faculty of Medicine de Saint-Etienne, University of Lyon, Lyon, France
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30
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Rand KH, Beal SG, Cherabuddi K, Couturier B, Lingenfelter B, Rindlisbacher C, Jones J, Houck HJ, Lessard KJ, Tremblay EE. Performance of a Semiquantitative Multiplex Bacterial and Viral PCR Panel Compared With Standard Microbiological Laboratory Results: 396 Patients Studied With the BioFire Pneumonia Panel. Open Forum Infect Dis 2020; 8:ofaa560. [PMID: 33447631 PMCID: PMC7793460 DOI: 10.1093/ofid/ofaa560] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/23/2020] [Indexed: 01/08/2023] Open
Abstract
Background Microbiologic results are critical to optimal management of patients with lower respiratory tract infection, but standard methods may take several days. The multiplex polymerase chain reaction BioFire Pneumonia (PN) panel detects 15 common bacterial species semiquantitatively as copy number/mL, 8 viral species, and 7 resistance genes in about an hour within the clinical laboratory. Methods We tested 396 unique endotracheal or bronchoalveolar lavage specimens with the BioFire Pneumonia panel and compared the bacterial detections to conventional gram stain and culture results. Results Of the 396 patients, 138 grew at least 1 bacterium that had a target on the PN panel, and 136/138 (98.6%) were detected by the panel. A total of 177 isolates were recovered in culture and the PN panel detected 174/177 (98.3%). A further 20% of patients had additional targets detected that were not found on standard culture (specificity 69%, positive predictive value 63%, and negative predictive value 98.9%). Copy number was strongly related to standard semiquantitative growth on plates reported by the laboratory (eg, 1+, 2+, 3+ growths) and was significantly higher in those specimens that grew a potential pathogen. Both higher copy number and bacterial detections found by the PN panel, but not found in culture, were strongly positively related to the level of white blood cells reported in the initial gram stain. Conclusions Higher copy number and bacterial detections by the PN panel are related to the host respiratory tract inflammatory response. If laboratories can achieve a rapid turnaround time, the PN panel should have a significant impact both on patient management and on antibiotic stewardship.
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Affiliation(s)
- Kenneth H Rand
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Stacy G Beal
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | | | | | | | | | - Jay Jones
- BioFire Diagnostics, Salt Lake City, Utah, USA
| | - Herbert J Houck
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Kylie J Lessard
- Department of Infection Prevention and Control, UF Health Shands Hospital, Gainesville, Florida, USA
| | - Elizabeth E Tremblay
- Department of Infection Prevention and Control, UF Health Shands Hospital, Gainesville, Florida, USA.,Florida State University College of Medicine, Tallahassee, Florida, USA
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31
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Oriano M, Gramegna A, Terranova L, Sotgiu G, Sulaiman I, Ruggiero L, Saderi L, Wu B, Chalmers JD, Segal LN, Marchisio P, Blasi F, Aliberti S. Sputum neutrophil elastase associates with microbiota and Pseudomonas aeruginosa in bronchiectasis. Eur Respir J 2020; 56:13993003.00769-2020. [PMID: 32499333 DOI: 10.1183/13993003.00769-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/19/2020] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Neutrophilic inflammation is a major driver of bronchiectasis pathophysiology, and neutrophil elastase activity is the most promising biomarker evaluated in sputum to date. How active neutrophil elastase correlates with the lung microbiome in bronchiectasis is still unexplored. We aimed to understand whether active neutrophil elastase is associated with low microbial diversity and distinct microbiome characteristics. METHODS An observational, cross-sectional study was conducted at the bronchiectasis programme of the Policlinico Hospital in Milan, Italy, where adults with bronchiectasis were enrolled between March 2017 and March 2019. Active neutrophil elastase was measured on sputum collected during stable state, microbiota analysed through 16S rRNA gene sequencing, molecular assessment of respiratory pathogens carried out through real-time PCR and clinical data collected. RESULTS Among 185 patients enrolled, decreasing α-diversity, evaluated through the Shannon entropy (ρ -0.37, p<0.00001) and Pielou's evenness (ρ -0.36, p<0.00001) and richness (ρ -0.33, p<0.00001), was significantly correlated with increasing elastase. A significant difference in median levels of Shannon entropy as detected between patients with neutrophil elastase ≥20 µg·mL-1 (median 3.82, interquartile range 2.20-4.96) versus neutrophil elastase <20 µg·mL-1 (4.88, 3.68-5.80; p<0.0001). A distinct microbiome was found in these two groups, mainly characterised by enrichment with Pseudomonas in the high-elastase group and with Streptococcus in the low-elastase group. Further confirmation of the association of Pseudomonas aeruginosa with elevated active neutrophil elastase was found based on standard culture and targeted real-time PCR. CONCLUSIONS High levels of active neutrophil elastase are associated to low microbiome diversity and specifically to P. aeruginosa infection.
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Affiliation(s)
- Martina Oriano
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy.,Dept of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Andrea Gramegna
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Leonardo Terranova
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Luca Ruggiero
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Laura Saderi
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Benjamin Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - James D Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Paola Marchisio
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Francesco Blasi
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Stefano Aliberti
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
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Shoar S, Musher DM. Etiology of community-acquired pneumonia in adults: a systematic review. Pneumonia (Nathan) 2020; 12:11. [PMID: 33024653 PMCID: PMC7533148 DOI: 10.1186/s41479-020-00074-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023] Open
Abstract
Background The etiology of community-acquired pneumonia (CAP) has evolved since the beginning of the antibiotic era. Recent guidelines encourage immediate empiric antibiotic treatment once a diagnosis of CAP is made. Concerns about treatment recommendations, on the one hand, and antibiotic stewardship, on the other, motivated this review of the medical literature on the etiology of CAP. Methods We conducted a systematic review of English-language literature on the etiology of CAP using methods defined by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We searched PubMed using a combination of the keywords ‘pneumonia’, ‘CAP’, ‘etiology’, ‘microbiology’, ‘bacteriology’, and ‘pathogen’. We examined articles on antibiotics that were develop to treat pneumonia. We reviewed all ‘related articles’ as well as studies referenced by those that came up in the search. After we excluded articles that did not give sufficient microbiological data or failed to meet other predetermined criteria, 146 studies remained. Data were stratified into diagnostic categories according to the microbiologic studies that were done; results are presented as the percentage in each category of all cases in which an etiology was established. Results Streptococcus pneumoniae remains the most common cause of CAP although declining in incidence; this decline has been greater in the US than elsewhere. Haemophilus influenzae is the second most common cause of CAP, followed by Staphylococcus aureus and Gram negative bacilli. The incidence of all bacteria as causes of CAP has declined because, with routine use of PCR for viruses, the denominator, cases with an established etiology, has increased. Viruses were reported on average in about 10% of cases, but recent PCR-based studies identified a respiratory virus in about 30% of cases of CAP, with substantial rates of viral/bacterial coinfection. Conclusion The results of this study justify current guidelines for initial empiric treatment of CAP. With pneumococcus and Haemophilus continuing to predominate, efforts at antibiotic stewardship might be enhanced by greater attention to the routine use of sputum Gram stain and culture. Because viral/bacterial coinfection is relatively common, the identification of a virus by PCR does not, by itself, allow for discontinuation of the antibiotic therapy.
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Affiliation(s)
- Saeed Shoar
- Medical Care Line (Infectious Disease Section), Michael E. DeBakey Veterans Affairs Medical Center, 2002 Holcombe Boulevard, Room 4B-370, Houston, TX 77030 USA
| | - Daniel M Musher
- Medical Care Line (Infectious Disease Section), Michael E. DeBakey Veterans Affairs Medical Center, 2002 Holcombe Boulevard, Room 4B-370, Houston, TX 77030 USA.,Department of Medicine, Baylor College of Medicine, Houston, TX 77030 USA
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Increased Respiratory Viral Detection and Symptom Burden Among Patients with Primary Antibody Deficiency: Results from the BIPAD Study. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2020; 9:735-744.e6. [PMID: 32841749 PMCID: PMC7442926 DOI: 10.1016/j.jaip.2020.08.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Patients with primary antibody deficiency (PAD) are at increased risk of respiratory tract infections, but our understanding of their nature and consequences remains limited. OBJECTIVE To define the symptomatic and microbial burden of upper airway infection in adults with PAD relative to age-matched controls. METHODS Prospective 12-month observational study consisting of a daily upper and lower airway symptom score alongside fortnightly nasal swab with molecular detection of 19 pathogen targets. RESULTS A total of 44 patients and 42 controls (including 34 household pairs) were recruited, providing more than 22,500 days of symptom scores and 1,496 nasal swabs. Swab and questionnaire compliance exceeded 70%. At enrollment, 64% of patients received prophylactic antibiotics, with a 34% prevalence of bronchiectasis. On average, patients with PAD experienced symptomatic respiratory exacerbations every 6 days compared with 6 weeks for controls, associated with significant impairment of respiratory-specific quality-of-life scores. Viral detections were associated with worsening of symptom scores from a participant's baseline. Patients with PAD had increased odds ratio (OR) for pathogen detection, particularly viral (OR, 2.73; 95% CI, 2.09-3.57), specifically human rhinovirus (OR, 3.60; 95% CI, 2.53-5.13) and parainfluenza (OR, 3.06; 95% CI, 1.25-7.50). Haemophilus influenzae and Streptococcus pneumoniae were also more frequent in PAD. Young child exposure, IgM deficiency, and presence of bronchiectasis were independent risk factors for viral detection. Prophylactic antibiotic use was associated with a lower risk of bacterial detection by PCR. CONCLUSIONS Patients with PAD have a significant respiratory symptom burden associated with increased viral infection frequency despite immunoglobulin replacement and prophylactic antibiotic use. This highlights a clear need for future therapeutic trials in the population with PAD, and informs future study design.
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Ogawa H, Kitsios GD, Iwata M, Terasawa T. Sputum Gram Stain for Bacterial Pathogen Diagnosis in Community-acquired Pneumonia: A Systematic Review and Bayesian Meta-analysis of Diagnostic Accuracy and Yield. Clin Infect Dis 2020; 71:499-513. [PMID: 31504334 PMCID: PMC7384319 DOI: 10.1093/cid/ciz876] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/02/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The clinical role of sputum Gram stain (SGS) in community-acquired pneumonia (CAP) diagnosis remains controversial. A 1996 meta-analysis of the diagnostic accuracy of SGS reported heterogeneous results. To update the available evidence, we performed a systematic review and a Bayesian standard and latent-class model meta-analysis. METHODS We searched Medline, Embase, and Cochrane Central by 23 August 2018 to identify studies reporting on the diagnostic accuracy, yield (percentage of patients with any pathogen[s] correctly identified by SGS), and clinical outcomes of SGS in adult patients with CAP. Two reviewers extracted the data. We quantitatively synthesized the diagnostic accuracy and yield, and descriptively analyzed other outcomes. RESULTS Twenty-four studies with 4533 patients were included. The methodological and reporting quality of the included studies was limited. When good-quality sputum specimens were selected, SGS had a summary sensitivity of 0.69 (95% credible interval [CrI], .56-.80) and specificity of 0.91 (CrI, .83-.96) for detecting Streptococcus pneumoniae, and a sensitivity of 0.76 (CrI, .60-.87) and specificity of 0.97 (CrI, .91-.99) for Haemophilus influenzae. Adjusted analyses accounting for imperfect reference standards provided higher-specificity estimates than the unadjusted analyses. Bacterial pathogens were identified in 73% (CrI, 26%-96%) of good-quality specimens, and 36% (CrI, 22%-53%) of all specimens regardless of quality. Evidence on other bacteria was sparse. CONCLUSIONS SGS was highly specific to diagnose S. pneumoniae and H. influenzae infections in patients with CAP. With good-quality specimens, SGS can provide clinically actionable information for pathogen-directed antibiotic therapies.
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Affiliation(s)
- Hiroaki Ogawa
- Department of Emergency and General Internal Medicine, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pennsylvania, United States of America
| | - Mitsunaga Iwata
- Department of Emergency and General Internal Medicine, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Teruhiko Terasawa
- Department of Emergency and General Internal Medicine, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
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Abstract
The phenomenon of attenuated antibacterial activity at inocula above those utilized for susceptibility testing is referred to as the inoculum effect. Although the inoculum effect has been reported for several decades, it is currently debatable whether the inoculum effect is clinically significant. The aim of the present review was to consolidate currently available evidence to summarize which β-lactam drug classes demonstrate an inoculum effect against specific bacterial pathogens. Review of the literature showed that the majority of studies that evaluated the inoculum effect of β-lactams were in vitro investigations of Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Haemophilus influenzae and Staphylococcus aureus. Across all five pathogens, cephalosporins consistently displayed observable inoculum effects in vitro, whereas carbapenems were less susceptible to an inoculum effect. A handful of animal studies were available that validated that the in vitro inoculum effect translates into attenuated pharmacodynamics of β-lactams in vivo. Only a few clinical investigations were available and suggested that an in vitro inoculum effect of cefazolin against MSSA may correspond to an increased likeliness of adverse clinical outcomes in patients receiving cefazolin for bacteraemia. The presence of β-lactamase enzymes was the primary mechanism responsible for an inoculum effect, but the observation of an inoculum effect in multiple pathogens lacking β-lactamase enzymes indicates that there are likely multiple mechanisms that may result in an inoculum effect. Further clinical studies are needed to better define whether interventions made in the clinic in response to organisms displaying an in vitro inoculum effect will optimize clinical outcomes.
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Affiliation(s)
- Justin R Lenhard
- California Northstate University College of Pharmacy, Elk Grove, CA, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
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Wang Z, Zang Y, Gao Y, Han L, Lin H, Gao Y, Chen M, Liu Y, Zhang Q, Fu E. Evaluation of bronchoalveolar lavage fluid combined with the loop-mediated isothermal amplification assay in lower respiratory tract infections. Am J Transl Res 2020; 12:4009-4016. [PMID: 32774754 PMCID: PMC7407691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
The clinical application of the loop-mediated isothermal amplification (LAMP) assay has been problematic because of conflicting results obtained from the LAMP assay and bacterial culture. In order to eliminate the interference of oral microorganisms and more accurately evaluate the diagnostic performance of the LAMP assay, we utilized bronchoalveolar lavage fluid (BALF) as a sample to test whether the LAMP assay and bacteria culture yielded similar results. A total of 1092 BALF samples from patients with suspected lower respiratory tract infections were collected. For each sample, parallel studies using both bacterial culture and the LAMP assay were carried out. We were the first to utilize BALF as a sample to study the consistency between the LAMP assay and bacterial culture results. The present study demonstrated that the positive rate from the LAMP assay was higher than that from bacterial culture, and the two methods had a better consistency than previously reported.
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Affiliation(s)
- Zaiqiang Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Yu Zang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Yanjun Gao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Luyao Han
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Hongwei Lin
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Yongheng Gao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Min Chen
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Yurou Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Qian Zhang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
| | - Enqing Fu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University Xi'an 710038, P. R. China
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Ma X, Li Y, Liang Y, Liu Y, Yu L, Li C, Liu Q, Chen L. Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia. BMC Microbiol 2020; 20:177. [PMID: 32576241 PMCID: PMC7310556 DOI: 10.1186/s12866-020-01842-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 06/03/2020] [Indexed: 01/25/2023] Open
Abstract
Background The rapid identification of pathogenic bacteria is important for determining an appropriate antimicrobial therapy for pneumonia, but traditional bacterial culture is time-consuming and labourious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneous detection of fifteen bacterial species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA genes and other specific genes of each pathogen were chosen as the amplification targets, amplified via multiplex polymerase chain reaction (PCR), and hybridized to oligonucleotide probes in a microarray. Results The DNA microarray detection limit was 103 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray, and 3 nontarget species from 4 clinical isolates were not detected. Additionally, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results for 99.4% (156/157) of clinical specimens were the same as those from a conventional assay. Conclusions We developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labour and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.
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Affiliation(s)
- Xiuqing Ma
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yanqin Li
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yuan Liang
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yang Liu
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Ling Yu
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Chunsun Li
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Qiqi Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Liangan Chen
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, China.
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Ngocho JS, Minja L, van der Gaast-de Jongh CE, Rahamat-Langendoen JC, Langereis JD, Mmbaga BT, de Jonge MI. Viral-bacterial (co-)occurrence in the upper airways and the risk of childhood pneumonia in resource-limited settings. J Infect 2020; 81:213-220. [PMID: 32533999 DOI: 10.1016/j.jinf.2020.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/31/2020] [Accepted: 06/06/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To examine the association between bacterial-viral co-occurrence in the nasopharynx and the risk of community acquired pneumonia (CAP) in young children living in resource-limited settings. METHODS A case-control study was conducted between January and December 2017 in Moshi, Tanzania. Children 2-59 months with CAP and healthy controls were enrolled. RSV and Influenza A/B were detected with a standardized polymerase chain reaction (PCR) method, and a simplified real-time quantitative PCR method, without sample pre-processing, was developed to detect bacterial pathogens in nasopharyngeal samples. RESULTS A total of 109 CAP patients and 324 healthy controls were enrolled. Co-detection of H. influenzae and S. pneumoniae in nasopharyngeal swabs was linked with higher odds of CAP (aOR=3.2, 95% CI=1.1-9.5). The majority of the H. influenzae isolated in cases and controls (95.8%) were non-typeable. Of the viruses examined, respiratory syncytial virus (RSV) was most common (n = 31, 7.2%) in cases and controls. Children with RSV had 8.4 times higher odds to develop pneumonia than healthy children (aOR=8.4, 95%CI= 3.2 - 22.1). CONCLUSIONS Co-occurence of H. influenzae and S. pneumoniae in the nasopharynx was strongly associated with CAP. The high prevalence of non-typeable H. influenzae might be a sign of replacement as a consequence of Haemophilus influenzae type b vaccination.
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Affiliation(s)
- James S Ngocho
- Kilimanjaro Christian Medical University College (KCMUCo), Box 2240, Moshi, Tanzania.
| | - Linda Minja
- Kilimanjaro Clinical Research Institute (KCRI), Box 2236, Moshi, Tanzania
| | - Christa E van der Gaast-de Jongh
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Janette C Rahamat-Langendoen
- Department of Medical Microbiology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jeroen D Langereis
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Blandina T Mmbaga
- Kilimanjaro Christian Medical University College (KCMUCo), Box 2240, Moshi, Tanzania; Kilimanjaro Clinical Research Institute (KCRI), Box 2236, Moshi, Tanzania
| | - Marien I de Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
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Hovold G, Lindberg U, Ljungberg JK, Shannon O, Påhlman LI. BPI-ANCA is expressed in the airways of cystic fibrosis patients and correlates to platelet numbers and Pseudomonas aeruginosa colonization. Respir Med 2020; 170:105994. [PMID: 32843162 DOI: 10.1016/j.rmed.2020.105994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Autoantibodies to bactericidal/permeability-increasing protein (BPI), BPI-ANCA, are often present in serum of patients with cystic fibrosis (CF), and correlate to airway colonization with Pseudomonas aeruginosa. The aim of the study was to investigate if BPI-ANCA IgA is also present in the airways of CF patients, and if its presence correlates with neutrophil counts, platelets, and P. aeruginosa DNA in sputum. METHODS BPI-ANCA IgA was quantified in serum and sputum samples from adult CF patients (n = 45) by ELISA. Sputum neutrophil counts, platelets, and platelet-neutrophil complexes were assessed by flow cytometry, and P. aeruginosa DNA was analysed with RT-PCR. RESULTS Serum BPI-ANCA IgA was present in 44% of the study participants, and this group also had significantly enhanced BPI-ANCA levels in sputum compared to serum negative patients. Sputum levels of BPI-ANCA IgA correlated with P. aeruginosa DNA (r = 0.63, p = 0.0003) and platelet counts in sputum (r = 0.60, p = 0.0002). CONCLUSIONS BPI-ANCA is expressed in the airways of CF patients and correlates with P. aeruginosa load and platelet counts, suggesting a link to airway inflammation and mucosal immunity.
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Affiliation(s)
- Gisela Hovold
- Lund University, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden
| | - Ulrika Lindberg
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Respiratory Medicine and Allergology, Lund, Sweden
| | - Johanna K Ljungberg
- Lund University, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden
| | - Oonagh Shannon
- Lund University, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden
| | - Lisa I Påhlman
- Lund University, Department of Clinical Sciences Lund, Division of Infection Medicine, Lund, Sweden; Skåne University Hospital, Division for Infectious Diseases, Lund, Sweden.
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40
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Edin A, Eilers H, Allard A. Evaluation of the Biofire Filmarray Pneumonia panel plus for lower respiratory tract infections. Infect Dis (Lond) 2020; 52:479-488. [PMID: 32319831 DOI: 10.1080/23744235.2020.1755053] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Background: Standard diagnostic methods for lower respiratory tract infections are currently too slow and insensitive to guide early clinical decisions concerning treatment and isolation. Syndrome-specific, diagnostic panels have potential to provide information about aetiology quickly. Available panels have been of limited use in lower respiratory tract infections due to slow turn-around-time, lack of quantification of important pathogens and lack of detection of resistance genes.Materials/methods: We evaluated the newly developed Biofire® Filmarray® Pneumonia Panel plus (Biomérieux). Eighty-eight consecutive lower respiratory tract samples were analyzed by both standard microbiological methods, as requested by the referring clinician, and by the panel. The agreement with standard methods, empirical treatment coverage and possible impact on isolation practices were assessed by comparing the results from standard diagnostic methods with the panel results in relation to clinical data and information of antimicrobial therapy.Results: Both qualitative and semi-quantitative results from the panel generally displayed good agreement with standard methods and by combining methods, a possible aetiology was detected in 73% of patients. Due to the panel approach, the panel detected viruses more frequently. In 25% of the 60 patients assessed for empirical treatment coverage, a pathogen not covered by current therapy was detected and in 30% of in-house patients the panel results were found to potentially influence clinical decisions related to isolation care.Conclusions: The new diagnostic panel shows promise in improving aetiological diagnostics of lower respiratory tract infections. Correctly applied it has potential to offer support in clinical decision-making within hours of sampling.
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Affiliation(s)
- Alicia Edin
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Anesthesiology and Intensive Care Medicine, Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Hinnerk Eilers
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Annika Allard
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
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Park GE, Peck KR, Ko JH, Kang CI, Cho SY, Chung DR, Lee NY. Clinical factors influencing the performance of bacterial multiplex polymerase chain reaction in patients with community-onset pneumonia. Eur J Clin Microbiol Infect Dis 2020; 39:1193-1199. [PMID: 32219584 DOI: 10.1007/s10096-019-03741-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/13/2019] [Indexed: 11/27/2022]
Abstract
The etiologic diagnostic yield of community-onset pneumonia (COP) using conventional methods is low. Bacterial multiplex polymerase chain reaction (mPCR) has been shown to be more sensitive than conventional methods. This study assessed the clinical factors influencing bacterial mPCR results in patients with COP. Patients with COP admitted to a tertiary care hospital between November 2015 and April 2016 were retrospectively assessed. Conventional methods included culture-based methods and serology for Mycoplasma pneumoniae. Bacterial mPCR that could identify Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, and Legionella pneumophilia was performed. Bacterial mPCR was performed in a total of 342 patients with COP in the study. Bacterial mPCR alone provided etiology in 99 patients. The total etiologic diagnosis rates improved from 22.2 to 51.1% when bacterial mPCR was added to conventional methods. Additional diagnostic benefits of bacterial mPCR were more prominent in the prior antibiotic non-exposure group (77.8% vs 63.5%, P = 0.015) and in the low-risk group with low CURB 65 score (62.6% vs 44.9%, P = 0.005). Patients who required ICU care, those with healthcare-associated pneumonia (HCAP), and patients with any underlying diseases were not associated with the additional pathogen detection rates using bacterial mPCR. By supplementing conventional diagnostic methods with bacterial mPCR-based methods, the overall pathogen detection rates improved in patients with COP. Moreover, the additional diagnostic usefulness of bacterial mPCR was significantly higher in patients without prior antibiotic exposure and in the mild-to-moderate-risk group with lower CURB 65 score.
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Affiliation(s)
- Ga Eun Park
- Division of Infectious Diseases, Department of Internal Medicine, Konkuk University Medical Center, Seoul, South Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06531, South Korea.
| | - Jae-Hoon Ko
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06531, South Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06531, South Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06531, South Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06531, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Yoo IY, Huh K, Shim HJ, Yun SA, Chung YN, Kang OK, Huh HJ, Lee NY. Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens. Int J Infect Dis 2020; 95:326-331. [PMID: 32179139 DOI: 10.1016/j.ijid.2020.03.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVES The performance of the investigational-use-only version of the BioFire FilmArray Pneumonia Panel (FA-Pneumo), a high-order nested multiplex PCR, was evaluated for the detection of typical respiratory bacterial pathogens and antibiotic resistance genes in sputa and endotracheal aspirate (ETA) specimens. METHODS Thirty-one sputa and 69 ETA specimens were analyzed. The diagnostic performance of FA-Pneumo was assessed using routine microbiological methods as the reference standard. RESULTS Overall sensitivity and specificity for organism detection using FA-Pneumo were 98.5% and 76.5%, respectively. The sensitivity for each pathogen was 100%, except for Klebsiella aerogenes, and the range of specificity was 83.3-99.0%. FA-Pneumo detected antimicrobial resistance genes in 17 out of 18 specimens (94.4%) that were resistant by antimicrobial susceptibility testing. FA-Pneumo additionally detected 25 resistance genes in 22 specimens, and sequencing for the presence of resistance genes confirmed the majority of these results (20/25, 80%). Semi-quantitative analysis of bacterial nucleic acid amounts by FA-Pneumo revealed that 88.2% of the identified bacteria (67/76) with ≥106 copies/ml also gave culture-positive results with significant amounts of bacteria. CONCLUSIONS FA-Pneumo is a rapid test with high sensitivity for the detection of bacteria and antimicrobial resistance genes in sputum and ETA specimens and could aid in determining antibiotic therapy.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases, Seoul, Republic of Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Yoo Na Chung
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - On Kyun Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Zhao D, Liu G, Wang X, Daraz U, Sun Q. Abundance of human pathogen genes in the phyllosphere of four landscape plants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 255:109933. [PMID: 32063310 DOI: 10.1016/j.jenvman.2019.109933] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
The surface of leaf, also known as phyllosphere, harbors diverse microbial communities which include both beneficial microorganisms promoting plants growth and harmful microorganisms, such as plant pathogens and human pathogens. Several studies have investigated the interaction between plants and human pathogens, while few works have focused on the quantitative analysis of pathogenic bacteria. On the basis of real-time polymerase chain reaction (qPCR), this study aimed to evaluate the abundance of following genes: the nuc and pvl of Staphylococcus aureus, the lytA and psaA of Streptococcus pneumoniae, and the ttr and invA of Salmonella enterica in the phyllosphere of four landscape plants (Nandina domestica, Rhododendron pulchrum, Photinia serrulata, and Cinnamomum camphora) growing in two habitats. Our results indicated that the relative abundance of pathogenic genes in the phyllosphere ranged from 10-9 to 10-6. The specific genes of S. aureus, S. pneumoniae and S. enterica in landscape plants were pvl, lytA and ttr, respectively. The two pathogenic genes of S. pneumoniae and the 16S rRNA gene were mainly affected by habitats, host species, and habitats-species interaction. Moreover, for the abundance of lytA and 16S rRNA, results showed that plants present in roadside with traffic pollution were relatively higher than that of campus with less pollution. The N. domestica and C. camphora were recommended for planting along the roadsides due to lower abundance of pathogenic genes. However, we have observed no significant difference in the abundance of pathogenic genes among four plants in the campus. Thereby, this study provided a valuable reference for selecting landscape plants in view of human health.
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Affiliation(s)
- Dandan Zhao
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Anhui Province Engineering Laboratory for Mine Ecological Remediation, China
| | - Guijia Liu
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Anhui Province Engineering Laboratory for Mine Ecological Remediation, China
| | - Xuefei Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Anhui Province Engineering Laboratory for Mine Ecological Remediation, China
| | - Umar Daraz
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Anhui Province Engineering Laboratory for Mine Ecological Remediation, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Anhui Province Engineering Laboratory for Mine Ecological Remediation, China.
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Jung J, Seo E, Yoo RN, Sung H, Lee J. Clinical significance of viral-bacterial codetection among young children with respiratory tract infections: Findings of RSV, influenza, adenoviral infections. Medicine (Baltimore) 2020; 99:e18504. [PMID: 31914021 PMCID: PMC6959858 DOI: 10.1097/md.0000000000018504] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We aimed to evaluate the clinical significance of bacterial coexistence and the coinfection dynamics between bacteria and respiratory viruses among young children. We retrospectively analyzed clinical data from children aged < 5 years hospitalized with a community-acquired single respiratory viral infection of influenza, adenovirus, or RSV during 2 recent consecutive influenza seasons. Remnant respiratory specimens were used for bacterial PCR targeting Moraxella catarrhalis, Haemophilus influenzae, Streptococcus pneumoniae, and Staphylococcus aureus.A total of 102 children were included; median age was 0.8 years and 44.1% had underlying comorbidities. Overall, 6.8% (7/102) of cases were classified as severe diseases requiring intensive care unit admission and/or mechanical ventilation and ranged from 8.8% for a patient with RSV and 7.6% for those with adenovirus to 0% for those with influenza viruses. The overall viral-bacterial codetection rate was 59.8% (61/102); M catarrhalis was the most frequent (33.3%), followed by H influenzae (31.4%). Influenza cases showed higher bacterial codetection rates (80.0%; 8/10) compared with those with adenoviruses (69.2%; 9/13) and RSV (55.7%; 44/79). S pneumoniae and H influenzae codetections were associated with reduced severity (aOR, 0.24; 95% CI, 0.07-0.89), and reduced risk of wheezing (aOR, 0.36; 95% CI, 0.13-0.98), respectively.We observed the interactions between respiratory viruses and bacteria and the clinical significance of viral-bacterial coexistence in upper airway on disease severity. Future study will be necessary to elucidate the active interactions between different viruses and bacteria and give clues to risk stratified strategy in the management of respiratory infections among young children.
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Affiliation(s)
- Jiwon Jung
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Euri Seo
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul
- Department of Pediatrics, Dongkuk University Ilsan Hospital, Ilsan
| | - Ree Nar Yoo
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - Hungseop Sung
- Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jina Lee
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul
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Liotti FM, Posteraro B, Mannu F, Carta F, Pantaleo A, De Angelis G, Menchinelli G, Spanu T, Fiori PL, Turrini F, Sanguinetti M. Development of a Multiplex PCR Platform for the Rapid Detection of Bacteria, Antibiotic Resistance, and Candida in Human Blood Samples. Front Cell Infect Microbiol 2019; 9:389. [PMID: 31799215 PMCID: PMC6863929 DOI: 10.3389/fcimb.2019.00389] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/29/2019] [Indexed: 12/29/2022] Open
Abstract
The diagnosis of bloodstream infections (BSIs) still relies on blood culture (BC), but low turnaround times may hinder the early initiation of an appropriate antimicrobial therapy, thus increasing the risk of infection-related death. We describe a direct and rapid multiplex PCR-based assay capable of detecting and identifying 16 bacterial and four Candida species, as well as three antibiotic-resistance determinants, in uncultured samples. Using whole-blood samples spiked with microorganisms at low densities, we found that the MicrobScan assay had a mean limit of detection of 15.1 ± 3.3 CFU of bacteria/Candida per ml of blood. When applied to positive BC samples, the assay allowed the sensitive and specific detection of BSI pathogens, including bla KPC-, mecA-, or vanA/vanB-positive bacteria. We evaluated the assay using prospectively collected blood samples from patients with suspected BSI. The sensitivity and specificity were 86.4 and 97.0%, respectively, among patients with positive BCs for the microorganisms targeted by the assay or patients fulfilling the criteria for infection. The mean times to positive or negative assay results were 5.3 ± 0.2 and 5.1 ± 0.1 h, respectively. Fifteen of 20 patients with MicrobScan assay-positive/BC-negative samples were receiving antimicrobial therapy. In conclusion, the MicrobScan assay is well suited to complement current diagnostic methods for BSIs.
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Affiliation(s)
- Flora Marzia Liotti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Brunella Posteraro
- Istituto di Patologia Medica e Semeiotica Medica, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | | | - Antonella Pantaleo
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giulia De Angelis
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giulia Menchinelli
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Teresa Spanu
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Pier Luigi Fiori
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Maurizio Sanguinetti
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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46
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ZHU CC, CUI JS, HU AZ, YANG K, ZHAO J, LIU Y, DENG GQ, ZHU L. Multiplex Nested Solid Phase PCR-Array Chip for Simultaneous Detection of Highly Pathogenic Microorganisms. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61199-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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47
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Pahlow S, Lehniger L, Hentschel S, Seise B, Braun SD, Ehricht R, Berg A, Popp J, Weber K. Rapid Isolation and Identification of Pneumonia-Associated Pathogens from Sputum Samples Combining an Innovative Sample Preparation Strategy and Array-Based Detection. ACS OMEGA 2019; 4:10362-10369. [PMID: 31460130 PMCID: PMC6648014 DOI: 10.1021/acsomega.9b00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/27/2019] [Indexed: 05/04/2023]
Abstract
With this study, an innovative and convenient enrichment and detection strategy for eight clinically relevant pneumonia pathogens, namely, Acinetobacter baumannii, Escherichia coli, Haemophilus influenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae is introduced. Bacteria were isolated from sputum samples with amine-modified particles exploiting pH-dependent electrostatic interactions between bacteria and the functionalized particle surface. Following this, an asymmetric polymerase chain reaction as well as subsequent stringent array-based hybridization with specific complementary capture probes were performed. Finally, results were visualized by an enzyme-induced silver nanoparticle deposition, providing stable endpoint signals and consequently an easy detection possibility. The assay was optimized using spiked samples of artificial sputum with different strains of the abovementioned bacterial species. Furthermore, actual patient sputum samples with S. pneumoniae were successfully analyzed. The presented approach offers great potential for the urgent need of a fast, specific, and reliable isolation and identification platform for important pneumonia pathogens, covering the complete process chain from sample preparation up to array-based detection within only 4 h.
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Affiliation(s)
- Susanne Pahlow
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
| | - Lydia Lehniger
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Stefanie Hentschel
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Barbara Seise
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Sascha D. Braun
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Abbott
(Alere Technologies GmbH), Research and Development, Loebstedter Str. 103-105, 07749 Jena, Germany
| | - Ralf Ehricht
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Abbott
(Alere Technologies GmbH), Research and Development, Loebstedter Str. 103-105, 07749 Jena, Germany
| | - Albrecht Berg
- INNOVENT
e.V. Jena, Prüssingstraße
27 B, 07745 Jena, Germany
| | - Jürgen Popp
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Karina Weber
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
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Lenhard JR, Smith NM, Quach CD, Nguyen TQ, Doan LH, Chau J. Bacterial brothers in arms: cooperation of Staphylococcus aureus and Pseudomonas aeruginosa during antimicrobial exposure. J Antimicrob Chemother 2019; 74:2657-2665. [DOI: 10.1093/jac/dkz247] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 05/03/2019] [Accepted: 05/16/2019] [Indexed: 12/23/2022] Open
Abstract
Abstract
Objectives
The optimal selection of antibacterials during polymicrobial infections is poorly defined. The objective of the current investigation was to quantify the pharmacodynamics of relevant antimicrobials during co-culture of Pseudomonas aeruginosa with two separate Staphylococcus aureus phenotypes.
Methods
Time–kill experiments were conducted against co-cultures of the P. aeruginosa strain PA01 paired with either the normal phenotype (NP) MRSA isolate COL or the small colony variant phenotype (SCVP) MRSA isolate Ia48. The killing by levofloxacin, gentamicin, clindamycin, vancomycin and polymyxin B was evaluated to investigate drugs with activity against one or both pathogens. A Hill-type function and a mechanism-based model were used to describe bacterial killing.
Results
P. aeruginosa attenuated the activity of clindamycin against NP MRSA, with a reduction in the Emax (maximal killing) from 3.67 (95% CI 2.79–4.56) in monoculture to 1.86 (95% CI 1.35–2.37) during co-culture, whereas a significant protective effect was not observed for other antibacterials. The reduction in NP MRSA killing by clindamycin was described well by a mechanism-based model that generated a maximal killing rate constant of clindamycin against the susceptible NP MRSA subpopulation of 0.267 h−1 in monoculture and 0.0395 h−1 in the presence of P. aeruginosa. During exposure to gentamicin, P. aeruginosa was the dominant organism in co-culture experiments regardless of the drug concentration or S. aureus phenotype; however, the SCVP MRSA was able to dominate the joint population beginning at a levofloxacin concentration of 1.5 mg/L.
Conclusions
The anti-staphylococcal activity of clindamycin was attenuated by the presence of P. aeruginosa.
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Affiliation(s)
- Justin R Lenhard
- California Northstate University College of Pharmacy, Elk Grove, CA, USA
| | - Nicholas M Smith
- Laboratory for Antimicrobial Dynamics, NYS Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
- School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Christine D Quach
- California Northstate University College of Pharmacy, Elk Grove, CA, USA
| | - Tuan Q Nguyen
- California Northstate University College of Pharmacy, Elk Grove, CA, USA
| | - Linh H Doan
- California Northstate University College of Pharmacy, Elk Grove, CA, USA
| | - Jeanette Chau
- California Northstate University College of Pharmacy, Elk Grove, CA, USA
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Comparison of Unyvero P55 Pneumonia Cartridge, in-house PCR and culture for the identification of respiratory pathogens and antibiotic resistance in bronchoalveolar lavage fluids in the critical care setting. Eur J Clin Microbiol Infect Dis 2019; 38:1171-1178. [PMID: 30859358 DOI: 10.1007/s10096-019-03526-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
Faster respiratory pathogen detection and antibiotic resistance identification are important in critical care due to the severity of illness, significant prior antibiotic exposure and infection control implications. Our objective was to compare the performance of the commercial Unyvero P55 Pneumonia Cartridge (Curetis AG) with routine bacterial culture methods and in-house bacterial multiplex real-time PCR assays. Seventy-four bronchoalveolar lavage specimens from patients admitted to a Scottish intensive care unit (ICU) over a 33-month period were tested prospectively by routine culture and viral PCR and retrospectively by Unyvero P55 and in-house bacterial PCR. Sensitivity/specificity was 56.9%/58.5% and 63.2%/54.8% for the Unyvero P55 and in-house bacterial PCR panels respectively; sensitivity for in-panel targets was 63.5 and 83.7% respectively. Additional organisms were detected by Unyvero P55 and in-house bacterial PCR panels in 16.2% specimens. Antibiotics were changed on the basis of routine test results in 48.3% cases; of these, true-positive or true-negative results would have been obtained earlier by Unyvero P55 or in-house bacterial PCR panel in 15 (53.6%) and 17 (60.7%) cases respectively. However, a false-negative molecular test result may have been acted upon in six (21.4%) cases with either assay. Sensitivity/specificity of Unyvero P55 antibiotic resistance detection was 18.8%/94.9% respectively. Molecular testing identified a number of respiratory pathogens in this patient cohort that were not grown in culture, but resistance detection was not a reliable tool for faster antibiotic modification. In their current set-up, molecular tests may only have benefit as additional tests in the ICU pneumonia setting.
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50
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Hassannejad N, Bahador A, Hayati Rudbari N, Modarressi MH, Parivar K. Comparison of OmpA Gene-Targeted Real-Time PCR with the Conventional Culture Method for Detection of Acinetobacter baumanii in Pneumonic BALB/c Mice. IRANIAN BIOMEDICAL JOURNAL 2019; 23. [PMID: 30665275 PMCID: PMC6707111 DOI: 10.29252/.23.2.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND Acinetobacter baumannii is an important pathogen in health care and is responsible for severe nosocomial and community-acquired pneumonia. To design novel therapeutic agents, a mouse model for A. baumannii pneumonia is essential. METHODS We described a mouse model of A. baumannii using clinical and 19606R standard strains for developing a quantitative real-time PCR (qRT-PCR) for rapid identification of A. baumannii infection from lung tissues of BALB/c mice. RESULTS To infect the mice, three doses of bacteria (0.5 × 108, 1 × 108, and 1.5 × 108 cfu/ml) were used. Lung tissues were cultured and compared with ompA gene. Clinical isolates had better positive results at day three with the highest dose than 19606 strain either in culture (4 versus 3) or in qRT-PCR (5 versus 4). However, qRT-PCR detection was 100%, the specificity was 70%, and the positive predictive value was 27%. CONCLUSION The qRT-PCR detection of A. baumannii in the BALB/c mice model has a higher sensitivity than the culture method.
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Affiliation(s)
- Niloofar Hassannejad
- Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran
| | - Abbas Bahador
- Dept. of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran; ,Co-correspondence: Abbas Bahador, Dept. of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Mobile: (+98-912) 2207431; E-mail:
| | - Nasim Hayati Rudbari
- Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran
| | | | - Kazem Parivar
- Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran; ,Corresponding Author: Kazem Parivar, Dept. of Cell Biology, Science and Research branch, Islamic Azad University, Tehran, Iran; Tel.: (+98-21) 44865179; E-mail:
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